This is my opinion and based on what I've played.
Two games that I feel do everything right it needs to.
Bioshock 2
It's story isn't as grand as the first, but this doesn't knock what the sequel goes for which is a quieter, more intimate tale. The gameplay was so much better with the dual-weapon/plasmid combination. Your choices with the Little Sisters was more involving with an actual relationship as you went about Rapture. The pacing is stronger and you're always moving forward to Inner Persephone.
The first BioShock, which I do love, jumped it's goals around of what the protagonist was supposed to be doing. I'll try not to spoil it. First, you crash in the middle of the ocean, enter a strange lighthouse above a destroyed city underwater and it's simple, help a man find his family and maybe he'll help you. But then that plan flops and this dude wants revenge now!
"Okay... sure, but, you're still gonna get me out of here, right?"
"Don't worry, the surface is waitin' fer us, but we can't let this go. My family, we'll make him pay!"
Escape. Revenge. Twist. Revenge again. Then. Finality. BioShock is stronger in some parts and it's sequel is more involved in others, but as a whole this small and loving story sticks with me more.
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Ratchet and Clank: Crack In Time
I can't find anything wrong with this and there's nothing that'd I want to go back and change. Fantastic weapons, the best story in the series, beautiful environments and levels, multiple costumes/skins, unlockables -- there's a lot of love here. Oh, and I can't forget the space radio station. Man, I loved that!