First, it's more than likely that they would simply use the shuttlecraft the same way we saw in "Enterprise", since that's really the only thing the transporter accomplishes anyway. The same thing basically happens in TFF, when the transporters aren't working so Kirk takes an assault team down in a shuttle. IOW, the transporter does exactly what a shuttlecraft does, it just does it faster and more conveniently but without giving you a nice mobile platform to keep your spare gear if you get stranded.Suppose for a moment if you will, that within the Trek universe, transporters were never invented for use with living beings (maybe cargo, and replicators would be fine) due to that pesky old Heisenberg Uncertainty Principle that no-one ever managed to devise some kind of compensator to work around.
Ignoring the real-world concerns of how it might change the franchise, or the various storylines that would be altered/impossible, etc, how does everyone imagine this would impact Starship (and I guess even Shuttlecraft!) design? Personally I suspect that many vessel classes might survive with little to no tampering - the Galaxy and Miranda classes seem like they have sufficient shuttlebay facilities already, but maybe the Constitution would end up needing a secondary bay up on the primary hull...
Thoughts anyone?
Secondly, there are situations where a shuttlecraft might not be ideal (inserting covert teams behind enemy lines or slipping in past enemy defenses) where transporters have a distinct advantage. In that case, it might actually be simpler to just have your away team sky dive from orbit (STXI on the drill) or drop them in some sort of insertion pods like ODSTs. Some sort of non-emergency version of the Kelvin Pod would seem to fit the bill.
As for the actual topic, I'm of the opinion that transporters are kind of over-used anyway. I'd prefer to build in more operational limitations to their use; it shouldn't be possible to beam through solid objects (e.g. rooftops, starship hulls, caves, etc), so if you need to beam an away team into an enemy ship you basically need to beam them onto the hull as close as possible to an airlock hatch. Same limitation for beaming up: line of sight or nothing. If you want to beam someone into a building or into a starship, then their transporter system needs to catch your beam and route them into their transporter room (otherwise, what the hell is the POINT of having a transporter room?)