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.