what does that first bit remind me of... errr... ah yes Sanitarium... where u loose ur memory... I think it should have some more of the confusion, loss of faith like in FO (u know like that bit at the end where he(she) got kicked out, that had quite an effect on me!)... u could have somthing like where ur a soldier (enclave?!) and u follow ur orders (kill what ever), then u start 2 c what things r really like... so u could change sides mid game (or closer 2 the start)...
How bout u start out by waking up on a medi-bed in some place, with no memory and u jus wander out and some shit happens 2 u!
Im not very imaginative u c (and i cant spell)