Beyond good and evil is not underrated, its just ignored by ubisoft. Every time theres any sort of sequel topic everyone wants a sequel of BG&E.
Alpha protocol was good.... but very buggy, like all obsidian games. It could use a sequel, or at least another game that's completely unrelated but uses the same systems.
Why do people hate Bioshock 2!? It's a great game! The only complaint I've ever heard is that you have to protect little sisters while they gather and I don't get it. It's a fun side quest thing that you can either do smash and bash style or sneaky trap layer or both. Or, you could just not do them, kill the little sister or just throw her in the closest hole, all you'd lose is a little adam. The only real weakness I see in that game is that, I at least, was ridiculously powerful in the final level and felt like I couldn't die, but that was probably due to my build being extremely tanky. Plus infinite made Bioshock 2 better because it hints that Delta is Dewitt which just makes the whole game more interesting.