You've got to remember where these are all from. Mods for other games. Most aren't canon (heck, some aren't even from the Trek universe at all). That said, there's a huge number of ships that are canon, that are noticeably absent from STO. Probably most notably is the Excelsior class, which was the workhorse of Starfleet for nearly a century before the last chronological series ended. Instead of the Excelsior class, they included the Constitution class, which was almost never, if it was even ever, seen even in TNG.
I agree. Where are all the ships we're used to? My nephue also wants to play with the U.S.S. Kelvin from the newest star trek movie. But, sadly, I had to tell him that they don't have it... at least not yet.