Enterprise NX-01 comes with no more than two (!) shuttles, as mentioned in ENT: "Terra Nova" and implicitly in "Impulse". This is unbelievably short-sighted on a starship built without a transporter as a regular means of transportation. We need to bear in mind that the transporter is only "experimental" and the crew is afraid of it. Realistically, Enterprise would have to rely even more heavily on the shuttle pods than seen in the show. But each of them can transport only six persons. And what about the cargo? I doubt that they would or could beam large amounts of food supplies. So what happens if one shuttle is defunct and the other one is on the way, just like it exactly happened in "Impulse"? Earth is several months away most of the time. Doug Drexler, designer of NX-01, has acknowledged the problem. He suggests: "In my opinion we have two pods that are on 'hot standby,' and two more that are 'mothballed' and can be made good to go in two days working normal shifts, one day working double shifts."
But the situation worsens again since we know that several times shuttles have been damaged, and may even have been a total loss:
|Episode||Situation||Definitely lost||Probably lost||Badly damaged|
|Terra Nova||Dropped into a cavern, no recovery mentioned||1|
|Breaking the Ice||Trapped in comet, recovered with Vulcan help||1|
|Shadows of P'Jem||Shot down, recovery uncertain||1|
|Shuttlepod One||Engine pod exploded, repair uncertain||1|
|Desert Crossing||Crash landed, recovery very unlikely (detection system)||1|
|Dawn||Shot down and abandoned||1|
|Cease Fire||Shot down, may have been damaged beyond repair||1|
|Impulse||Took heavy beating in an asteroid field||1|
|Storm Front||Destroyed on ground near New York in 1944||1|
Considering that Shuttlepod One reappeared briefly after it had been left behind on the moon in ENT: "Dawn", I'm not taking into account the shuttle numbers. Maybe the registry on another shuttle (if there was any left intact) was simply repainted.
The frequency of shuttle accidents unpleasantly reminds us of Voyager's shuttle losses (up to 17 altogether). But unlike the 24th century ship Enterprise doesn't have replicator technology (unless shuttles were replaced or repaired at the station in "Dead Stop"). With at least one shuttle lost and likely the rest more or less damaged towards the end of season two, it is about time for Enterprise to return to Earth for resupply. This has probably happened in "The Expanse". But the short-sightedness of first giving the ship too few shuttles and then crash them frequently sheds a bad light on the authors and producers who seem to have learned nothing since Voyager in terms of consistency. Not to mention the lack of creativity in all the shuttle accident stories.
The question whether Enterprise could already have a transporter in the first place is discussed here.
Now that the technology is introduced and "approved of for biomatter transport" sooner than expected, we should expect that the transporter would be more than just decoration and would be used frequently -- at least in case of an emergency when a shuttle could not be used or was too slow.
Here are the episodes with transporter activity and how and why it is used.
"Broken Bow": Archer is beamed off the Suliban Helix although it is considered extremely unsafe; a shuttle would be too slow.
"Strange New World": The transporter is used to beam up Novakovich because a shuttle is unable to lift off or land during a storm.
"The Andorian Incident": Three security officers are beamed to the monastery to free the hostages, for a shuttle would be detected too easily.
"Civilization": The Malurian reactor is beamed up from the surface, and then beamed into space. No beaming of personnel.
"Detained": The transporter is used to send a communicator to Archer in the prison and to beam down Reed, disguised as a Suliban.
"Vanishing Point": The transporter is utilized after a long time to rescue Tucker and Hoshi from a polaric storm. Hoshi is the victim of the first transporter accident.
"Anomaly": The stolen cargo is beamed back to the ship. No visible beaming of personnel.
"Extinction": Tucker and some MACOs are beamed down to rescue the mutated crew members.
"Impulse": Trellium is beamed aboard. No beaming of personnel.
"The Shipment": A tube with kemocite is beamed to and from the ship. No beaming of personnel.
"North Star": Archer and Bethany are beamed up to escape the sheriff's gun.
"Chosen Realm": Pretending that the transporter is used for waste disposal, Archer fabricates his own execution.
"Hatchery": The transporter is used to overwhelm Archer in the hatchery.
"Damage": The boarding party is beamed over to the alien ship to steal the "warp coil".
"E2": No personnel transport, just the beam-over of power conduits of E2.
"Countdown": Five crew members, two at a time, are beamed out with the damaged transporter from the Insectoid vessel. Hayes is shot into his chest while he is being beamed out and dies later.
"Storm Front": The transporter is consequently and frequently used to beam down and beam up personnel.
"Borderland": Crew members are rescued from the Orion slave market after they have been located. Soong disables his transponder and can't be simply beamed up.
"Cold Station 12": A boarding party is beamed to Cold Station 12. How this can be accomplished with Enterprise staying out of the system (Soong can monitor the ship when it was still millions of miles away) remains a mystery though.
"The Augments": The radiation from the station's core does not allow to use the transporter to rescue Archer, so he is beamed out from space after decompressing the maintenance shaft.
"The Forge": The transporter is used for the emergency beam-out of Malcolm and Travis from the destroyed Federation Embassy.
"Babel One": Trip, Malcolm and the MACOs are beamed over to the Romulan marauder.
"In a Mirror, Darkly": Just for the sake of completeness, in this Mirror Universe episode the transporter is consequently used in tactical operations.
Transporter not used, with a reason
These are the episodes in which the transporter is not used, and either a reason was explicitly mentioned, or we may easily make up one.
"Terra Nova": Rescue of Malcolm Reed from the caves of Terra Nova. The transporter is not capable of penetrating the rock, Reed is too deep beneath the surface, as Tucker mentions.
"Shadows of P'Jem": Rescue of Archer and T'Pol from the Coridan rebels. Tucker and Reed don't have clear lifeform readings when they go down with the shuttlepod, so the transporter is obviously no option.
"Sleeping Dogs": Emergency beam-out of Hoshi, T'Pol and Malcolm from the Klingon ship. Mayweather mentions that no transporter lock is possible because of the heavy interference.
"Desert Crossing": Rescue of Archer and Tucker from the desert. There is an "orbital dispersion field" field present, and they can't be located.
"Shockwave, Part 1": Infiltration of the Suliban stealth cruiser using the transporter after taking down the cloak. We may make up a few reasons why using the shuttle is safer or easier, although Reed always has quite detailed scans of its interior.
"Cease Fire": It would be an option to rescue the hostages with the transporter. No reason is mentioned why this wasn't possible, but the Andorians may block the transporter.
"Dawn": The isotopes in the atmosphere of the planet obstruct the simple emergency transmitter, whereas the incredibly more complex transporter would be able to beam up Trip and the Arkonian pilot. The transporter is not used, however, because the sudden temperature change would kill the Arkonian who is in an extremely dehydrated state on the hot surface on the planet. We only have to wonder if the inside of the shuttle that brings him back is extremely heated up in order to avert the imminent temperature shock.
"Canamar": Reed manages to pick up Archer's and Tucker's biosigns on the prisoner transport, but the Enaran official objects he can't use the transporter because the ship is heavily shielded.
"Extinction": The transporter is considered an option, but is not used because there is no possibility to contain the virus. In other words, there is no biofilter yet.
"Divergence": When Archer and Reed discuss how to get Trip onto the ship at warp, the possibility of beaming him over is expressly ruled out.
Transporter not used, without a reason
These are the episodes in which the transporter is not used and is not even considered an option, although an emergency situation would require it.
"Breaking the Ice": Rescue of Reed and Mayweather from the crashed shuttle prior to the risky salvage of the shuttle itself. There is nothing in the simple asteroid that should block the transporter. The grappler is not safe at all considering the ice coating on the shuttle hull, but they keep trying. These attempts look very risky even compared to the "unsafe" transporter. They should beam out at least Travis who is injured.
"Fortunate Son": Beam-out of the Nausicaan hostage from the E.C.S. Fortunate. This would resolve the conflict much easier.
"Detained": Rescue of Archer and Mayweather from the Tandaran prison. This should be possible, since Reed manages to beam down with ease, and it would be less risky than letting Tucker land with the shuttle to retrieve them. The Suliban prisoners are left to themselves and board their own shuttles anyway. The only half-way reasonable explanation is that Enterprise has to pull back to a higher orbit when Trip attacks the prison with the shuttle.
"Minefield": Rescue of Reed whose leg has been penetrated by the mine's tentacle. This would have set off the detonation. On the other hand, it should have been possible to beam Archer and Reed aboard immediately after the explosion, instead of trying to "fish" them from space, which is awfully unrealistic. Well, the transporter may be offline after the detonation of the first mine.
"Marauders": Using the transporter against the Klingon marauders. At some point, it must be advantageous to beam down a security squad to surprise the Klingons, rather than engaging in possibly lethal hand-to-hand combat with them. But fortune favors the fools. The Klingons are stupid enough to fall for the crude tricks prepared to overpower them.
"The Communicator": Rescue of Archer and Reed who are facing their execution. This is the most blatant transporter ignorance of the series. There is absolutely no reason not to use the transporter, especially since the low technology on the planet wouldn't have provided any counter-measures.
"Regeneration": Rescue of the Tarkaleans from their damaged vessel. Although time is pressing because of the "minimal life support" on the ship and because Enterprise needs to continue pursuit of the Borgified transport, nobody considers to use the transporter.
"The Xindi": Rescue of Archer, Tucker and the Xindi. Reed and the MACO major never think of using the transporter either to beam up the hostages or to beam down the rescue team.
"Observer Effect": It would have been easier to beam out Hoshi and Trip from the quarantine area than going there in spacesuits, possible losing precious time to save them. Well, unless the quarantine area is shielded against the transporter. This is not hinted at, though.
Summarizing, considering that it would have been better to use the "unsafe" transporter instead of letting someone die, there are a few cases of careless writing. Fortunately, the tendency is not yet strong enough to allow the interpretation that the producers or episode authors intentionally "forgot" the transporter out of a strange feeling of remorse because they introduced the technology prematurely.
Enterprise Continuity Problems - where the series is in contradiction to established history
Thanks to Keith Ichinaga for the suggestion to care about shuttle crashes, to Graham Kennedy for reminding me of the crash in "Desert Crossing" and the repair station in "Dead Stop", to Christian for a correction about "Dawn", to Jason Bullock for another necessary correction, to James Stewart for a correction about the transporter, to Mark Johnson for another transporter use and to Tim Smith for trying to find rationales for the non-use of the transporter.