My 10 best (not in any order) and you can put them in whatever category and 1 per franchise
1. Ratchet and Clank: A Crack in Time
2. Uncharted 3
3. Infamous
4. God of War 3
5. The Last of Us
6. Resistance 3
7. MGS4
8. Batman Arkham City
9. Heavy Rain
10. Smash Bros. Brawl
Puppeteer looks like it's about to penetrate those ranks though and Beyond seems like it could replace Heavy Rain as the most immersive story this gen (well maybe Last of Us now). Also GTA5 could impress but there's just too many to count.