Well, the only way to compare two games is by all the features you have in each, something you can measure; "fun" isn't a quantitative value. You can't definitively say "PROTOTYPE MAOR FUNZ" or "COD5 R0XX0RZ LOL", since there's pretty much no similarity between the two and since everyone would have differing views/opinions about which is more fun.
IMO, Prototype is more unique. FPS has been beaten to death with a dead horse since like 2004. If you've already played other COD games, especially COD4, you're not really missing out if you don't buy COD5.