Yeah, I think the whole 'who are you' line made people pretty angry for a while but now the dust has settled i think people are starting to see he could ba maybe just a bit confused, especially since the line before was him commenting how real his 'dream' had felt.
Personally I liked the final, right up until the end. It wasnt even the 'amnesia' thing that ruined it, it was just that the end totally contradicted the feel of the rest of the episode and it felt a bit disjointed, that and I dont think cliff-hangers really suit Bones, they're still pretty much a stand-alone story kind of show so any major continuation doesnt really work as far as I'm concerned