Okay, the "Guardian of Forever" storyline... One thing I don't like, another I don't understand:
1. All those past Klingon ships (D7's, for example) should get creamed by your ship.
--Think back to any time in ST when they encountered an older generation ship, the thing was always ridiculously outclassed. So should these be. If it's "too easy," just have more of them there.
Would make the player feel heroic, and also frame their own ship in a manner to really appreciate your advancement. Many games do this, and it usually works well. (most recently, in Dragon Age, where towards the end you just mow down enemies; it really lets you see how far you've grown through the game)
2. The timeline is NOT restored -- it's SCREWED UP!
-- They take Paris' DNA to "restore" the original Klingon genome before the augment contamination, the change what made them the Klingons as we've always known them, as they were on TOS, and possibly what allowed Kittomer to ultimately occur.
W/o the augment DNA, they never would have "settled down" and become more clear and peaceful; they would've remained purely warlike.