Because they wanted a different story, FWIR it was the first thing they said. A new era that they could write their own stuff for. It the exact same premise as Trek XI. A TNG MMO would bore the crap out of the MMO community. Why? Because it's slow and about diplomacy, and understanding the human mind. With a market as competitive as the Massiley Multiplayer one, it needs to be fast, simple, and 2.0 friendly. That's why there are only 3 major archetypes with a little bit of freedom in them.
It breaks down like this: If you have designated Tank, Mez, Healer, Buff, DPS, Burst and Ranged (Let's face it, why would Trek ever have melee in space battles?) It gets too complicated for the general gaming community, and only interests (Depending on complexity and diversity of classes) either A: People who played Everquest (*Waves hands* I did!) or Trek fans who like things impossibly hard for the sake of getting the "Trek Experience".
This game holds a bit of both worlds, in that it has the absolute fundamentals for a decent RPG party (Tank, A Mez/Heal/Buff combo and DPS), that can be opened up to suit your liking, and at the same time it keeps the Trek look, with the customization that Cryptic are expected to add into their games now (City of Heroes/Villains/Going Rogue, Champions Online), and two forms of combat as opposed to one, which really, should make it a lot harder to get bored of levelling, which is a common problem with all level-based RPGs in general.
As for your complaint about the Borg, they never really said they were wiped out, IIRC. They took out Unimatrix-0, or something like that. It's way out into the Future, and no doubt they've got a new queen or something to keep the hive under control. Think of Borg like ants or bee's or whatever. They can't get rid of them either because they were what put the "Oomfph" into TNG, and more notably Voyager, and kept it alive for so long (That and Jeri Ryan). There are only so many stories one can make up, especially when you have a vicious pack of fans like Trekkies who will complain about the tiniest things (As parodied in just about everything. Simpsons, Futurama, almost every sitcom ever made, and definitely Big Bang Theory).
tl;dr: Future timeline to give some creative liberties to the writers while keeping an established universe/canvas to work on, while appeasing to fans of the series. And it seems to be working, too. Look how much attention this thread has gotten.
EDIT: To add to Darkthunders post: If you hate having a ship that looks old and supposedly "uncanon" or whatever. Make your own. There are miranda variants they've shown that look only barely like their original design.
Hell, that's what everyone here does anyway, right? Dream up and try to create our own vision of trek neatly wrapped in a grey hull. ;)
