Yeah, Brotherhood's ending was way too abrupt, but that seems to be the series' M.O. It'll have a satisfactory ending one of these days! Hopefully Revelations will be it. The Desmond stuff was better in Brotherhood, at least.
I'm not sure I'm too keen on all the "Pieces of Eden" and all it entails as far as AC's storyline goes. It takes it from "Cool game set during real historical time periods" to "Uhhhhhhhhhhhh what is going on here"
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"The great GF...Bahamut."
"...GF? I...? Using my powers...It is you humans...I fear..."