I haven't heard or seen it, either it's because I'm a Commander or it isn't in the game yet.

It's not in the game at the moment, unless you count the Mirrorverse mission.

I don't even recall it being mentioned.

I don't think it's possible to include the Enterprise right now and make it something that stands out. It would still be the Sovereign class Enterprise-E and since there are so many other Sovereign class ships running around, the Sovereign class has lost a lot of what made it such a striking figure in the films - it was unique, edgy, and incorporated a lot of darker Starfleet that was introduced in DS9.

They have a mission where you go back in time and come across the 23rd century enterprise.

For what it's worth, it's mentioned in the loading screens that Data is now Captain of the Enterprise-E, which also confirms that the efforts started at the end of Nemesis worked out, or at least that's my theory

Yes, the novel has a chapter with Geordi talking about Data's return.

Also Data was seen captaining the Enterprise-E in the Star Trek Countdown comic, that led into the new film: Captain Data 1 & Captain Data 2.

Which enterprise? there have been a few of them.
NX-01
Original <-- is in the game
A
B
C
D
E <-- is the one your talking about right?