I beat the game twice in early access: the second time I had a full fleet of T3 ships (they had no problem), and my secondary officers were running around in the hand-me-down T2's. The first time, I had two sets of T2 fleets, which somehow managed to knock off the Chruul support fleets using a Tac-Eng1-Eng2 combo. I then proceeded to lose both T2 fleets, one T1 fleet, and one or two fleets of shuttles in my successful attempt to beat the Chimera.
Moral: if you choose T2 fleets, research all the upgrades on the ships that you are using.