Still, the mystery behind you and your existence is incredbly compelling, and the final ending is one gigantic mindfuck which makes you shed a tear for the sheer hopelessness of the situation - no thanks to you and your security guard/turret murdering spree.
I think this is pretty much spot on. Trying to guestimate where to grab a ledge... ouch. The gun combat was utterly one-sided, with you taking the odd random damage.
IMO, the first episode was the strongest, mainly due to the way stories of this kind work. They're always most interesting when you're being teased with information, the truth tends to be more mundane, and episode 2 was a little heavy-handed in its convenient exposition terminals. Thankfully episode 3 returned us to a more personal terminal.
However, the ending was absolutely superb. Didn't see it coming at all. Alternate was nice too, and it doesn't take too long to replay the level the second time.
Could have done without the boss fights though. Boss fights suck because most are simply a minute of spotting the pattern but then several minutes of waiting around for the specific weakness to expose itself. Your brain switches off and goes elsewhere for these segments. The last was the worst since the buttons necessary don't seem very obvious, they looked like arrows to me and I took them as hints of the existence of platforms in the rooms centre, which weren't obvious either.
Still, the gameplay made for a fun diversion, but it was really the story which drove it on. Strongest in part one due to discovery (and apart from Planescape Torment, I can't think of an amnesia game which got stronger as you find out more), with definitely the best atmosphere (if a little too much back and forth) but an ending which really gets you, and was superbly built-up... you think you've got it all, and then the game smacks you in the face.
Only story weakness I can think of is your identify reveal. Left me cold and I wondered why it was there.