I liked the way the story ended. It basically could be seen as leading directly into MTMTE - Prime has ordered the evacuation of Cybertron and Megatron is severely peeved at him for spoiling his plans. Cue Ark vs. Nemesis space battle and crashing into Earth  

Fight-wise, I think I preferred the end of the Decepticon campaign to the end of the Autobot one, partly because I have more memory of Omega Supreme (I had the VHS release of Key to Vector Sigma / War Dawn as a kid and watched it endlessly  ), and partly because I have no real attachment to Trypticon as a character.

 

I loved the game.
Absolutely loved it and the campaign had some fantastic moments.

But either Megatron and Optimus had a history, or they never met.
I don't know and the fact that there was no Optimus VS Megatron fight in the game was a big disappointment.