I own all the Trek micro machines except for the H.M.S. Bounty (the BoP that had adjustable wings). I agree about their awesomeness and that they were cut short before their time (although I still scratch my head as to why the Saratoga doesn't have its side guns, or why the Stargazer is yellow to match the desktop model and not gray to match the studio model...).
As to who was in charge of selecting them...who knows? But yeah, some of their choices were just bizarre...I mean, the Numiri ship? Who the hell were they?
I think the problem at the time was that during both DS9 and VOY, both series had lots of one-off aliens and not a lot of new Starfleet, Klingon, or Romulan ships other than what we saw in TNG. Plus, the Akira, Saber, Steamrunner and Norway class ships were seen so briefly, and had zero info about them at the time, that I can understand their omission (but there's really no excuse for not having the Phoenix or the T'Plana'hath IMHO...)
Also, they could have made another three-pack of TOS with the Tholian ship, the Aurora, and the Fesarius. The Merchantman would have been another good choice (I remember FASA's miniature of that ship, and it was quite cool-looking). Ditto your feeling about the Jenolan. I also wouldn't have minded seeing the original large TNG shuttlecraft, a workbee, a travel pod, Regula One, and the Bozeman.
Numiri were from season one's "Ex Post Facto". Like most alien ship models, it was modified and used many times both before and after as a "ship of the week". (Check out the Studio Models pages on Memory Alpha).
Same goes for the other one-shot ships I mentioned. One upside to this, however, is you can pretend a Klaestron ship is a T'Lani ship, or Tamarian ship, or even a totally new alien ship.
Why did the Saratoga lack the "guns" (if that's what they were)? Not sure. Perhaps they simply took a look at the studio model and assumed it was simply a Reliant look-alike without the roll bar. Interestingly, though, they didn't use the same molds they did for Reliant. The Saratoga's noticeably thicker.
I think you gotta give them a pass for not making any "First Contact" ships, other than the big "E": Being the "hero" ship, the E was almost certainly designed long before any other ships from the movie. It's likely Galoob's time making Star Trek ships ran out around that time, meaning any other ships from the movie probably would've been too late. (Possibly true of the Groumall and Vidiian ship as well, both of which, I think, were first seen in spring of '96).
The yellow Stargazer was clearly because the Ready Room model got a hell of a lot more screen time than the studio model. In fact, the packaging on the back shows the incorrect registry (NCC-7100) that the Ready Room Stargazer had.
A Merchantman would be nice. Same goes for a Tholian ship (since they were the same model, I doubt they'd to an Aurora). Forgot to add earlier that a Maquis/Federation fighter would be nice too. I agree with Regula One. That smaller Cardassian ship (I think they're called Hideki class) would've been a better choice than the Keldon Class. And, yes a Jenolan wouldn't have been bad either. A T'Pau too.
Honestly, I don't need to see all that many types of shuttles, though. I think the Galileo, the TNG shuttle, and the Voyager shuttle are enough. The Spacedock shuttle didn't excite me (especially when they could've made a Merchantman instead). Seeing other TNG shuttles, the travel pod, or a Workbee really didn't interest me. I'm not sure a Fesarius would work either.
I don't a problem with it myself, but I'm not sure they'd bother with the Bozeman, after doing two other VERY similar looking ships.