I have all but 3 of them myself - the rare(r) Kazon ship, Caretaker array, and Bajoran Solar ship. Have a couple doubles too. Runabouts, DS9, Cardassian Galor. Still have them all. Recently bought a couple loose for my nephew, cause he wanted some ships to play with and it was really tough to find one that where both affordable and durable enough to stand up to kid play.
I'm a ship junkie though. I've got the Furuta ships too, and all the Hallmark ornaments, and the Playmates ones, and the Art Asylum/DST ones...
Very few ships exist in physical form I don't have. Cause I just have to have them. Even spent the $75 or so for a Luna-Class (USS Titan) resin model.
I wish they'd make micro-machines again.
Prometheus, Steamrunner, Akira, Saber, Norway, Nova, Yeager, Delta Flyer, Borg Sphere, Borg Queen Diamond, Borg Tactical Cube, Borg Probe, Jem'Hadar Warship (bigger Jem ship, not the attack one we have), Cardassian Heidki, Breen Warship, Romulan Valdore, E-E (cause the one they did in the day isn't accurate, tbh), E-E shuttle from Nemesis, nuTrek 1701, nuTrek Kelvin, NX-01, Andorian Kumari, both (or all 3?) Vulcan ENT ships, ENT Shuttle pod, ENT Romulan BoP, ENT Klingon Raptor...
Just to name a few...
If they'd kept up at the rate they were going, we might've had a fourth, fifth, or even sixth collector's set by the time "Enterprise".
That being said, every set had at least a few "hero" craft (1701, 1701-A, 1701-D, DS9, and arguably the runabout in the first set; Defiant, and 2 versions of the "D" in second set, Voyager and the "E" in the third). Most of the rest were ships from well-known aliens (Klingons, Romulans, Cardassians, Kazon, etc.) or ships that were prominent in a movie (Reliant, Excelsior, Enterprise-B, etc.) or a few of the more notable one-shot Starfleet ships (Enterprise-C, Stargazer, Pasteur, Saratoga).
By the time of the third set, they were getting into some more obscure alien-of-the-week ships (Karemma, Klaestron, Numiri) that might not have sold so well. There were a couple more Dominion ships they could've done and maybe some from "First Contact" and "Insurrection" but I'm not sure what other "hero" ships they could've done, other than the Delta Flyer and arguably the Phoenix, between 1996 and 2001, when "Enterprise" started.
I wouldn't have minded the starships from "First Contact", but their time on screen was pretty brief. "Voyager" was pretty much all "ship of the week" stuff for most of its latter half, with not too many standouts, except, ironically, for Starfleet stuff like the Prometheus, the Equinox and the pseudo-Starfleet Dauntless.
Now they had a few good ones again once "Enterprise" started: NX-01, obviously, plus Vulcan, Andorian, and Klingon ships. (I supposed they'd do a shuttlepod, but the truth is I could take or leave most shuttles). Still, several years long wait for a toy company, especially since most of those ships' first appearances were pretty far apart.
I really liked Abrams' Trek, but I honestly don't have any interest in ships from that series, just like I'm not interested in miniatures from the Star Wars prequels.
There were some I would've liked, but maybe in retrospect, we didn't miss as much as we think.