I love the idea of T1 PvP play though. Maybe I'll have to approach my fleet about that, though I wouldn't buy a Zen store ship just for that. I was actually thinking this morning about a shuttle only queue (can't play the Vault shuttle event yet), but that's another thread entirely.
We've done shuttles too, that's nutty. We've also done 5-10 shuttles vs. one guy in his T5 ship. Actually managed to bring down an Armitage 3 times with 6 shuttles before he racked up 15 kills, lol.
As for the main derailment of this thread, Cryptic has already put explanation for that into the game. Specifically, if you look at the NX replica (not, it's specifically a replica), it says tech has advanced enough that they can basically make the ship however they want. It's a similar excuse as used in Galaxy Express 999 for why anybody could or would make interstellar spacecraft that look like old time steam trains.
Is it a contrivance just to allow people to play their favorite ship regardless of the setting? Yes, absolutely. We aren't going to be able to have Star Trek Enterprise: Online, Star Trek TOS: Online, Star Trek TNG: Online and Star Trek 2409 Online. This one game has to satisfy everybody. It's just a video game, and its status as soft canon is highly debatable, so who cares. I doubt the authors of the Pocket novels will start having technologically modern Excelsiors showing up in post-Nemesis relaunch stuff just because STO did it. So yes, it's a contrivance, yes it doesn't make sense in universe if you think about it, but just roll with it. From a gameplay POV it doesn't matter.