Well, I'm diggin' all this stuff... thanks!
My thoughts re: these shuttles, albeit not quite 100% in line with yours (I THINK)... it goes in large part to my take on "FTL impulse" (which is what I think the shuttles have). That is, that the nacelles are subspace field generators but not WARP DRIVE engines... you get FTL by putting the shuttle in a static subspace bubble and using impulse within that bubble.
Now, I remember the shuttle we saw in STVI... no external nacelles, used to move from surface to spacedock. That's what I'd be inclined to go for.
Basically, take a TOS-type shuttle, remove the "outriggers" nacelles, increase the impulse section size to about 150% or 200% of what's there now, and reduce the crew compartment by the same amount (so that the shuttle is the same size).
This would probably remove the last row of seats... a 5-man rather than 7-man shuttle.
I also thin that the nose might be a little more "sharp." Inside, it would be a bit more mechanical and less "clean and sterile" but for the most part very similar to the TOS shuttle we know (and that you've gone into in such detail).
One point I've brought up before... the "curved in towards the centerline" sections atthe top of the hull side panels. What are they for? Well, I've always assume that these were rails... so that a "crane in from above" system could have something to latch on to. Yes, I know people are thinking I'm borrowing this from "Enterprise" but I'm not... ENTERPRISE borrowed this from M.J.'s original thoughts on the concept. So even if you hate "Enterprise" with a passion, this approach shouldn't be rejected out-of-hand.
Ah, you say... but the Enterprise 1701 didn't need that. Yes, that's true... but the fleet is made up of MANY vessels, and it's unreasonable to assume that Starfleet would put shuttles on one ship that would be INCAPABLE of interacting with any other ship, or with any other base for that matter.
So, keep the "docking rails" on the top, the same basic shape, the same basic impulse configuration... totally alter the landing gear (actually, I think something like your nose-gear version, above, would work great here, with the rear gear coming off from under the wings, not from the nacelles).
I don't know if having folding wings is useful or not... I'd probably go with them (and, again, not because of Enterprise but because it's a common practice in REAL carrier-based aircraft, and I'm assuming that the subspace field's mass-reduction in later shuttles made the use of aerodynamics less necessary in shuttle design!).
Anyway, just a few more cents for ya... far more than two, by now...
