after thinking about it for about five seconds i've come up with the reasons that waters is starting/playing too much:
--sams got hurt. he missed a lot of practice during camp so the snyder/dimel/miller machine got used to seeing waters back there. they game planned thinking of waters as their qb.
--del miller. you're aware of this, but don't forget how much of a hard on del has for waters. del is also the passing game coordinator, and best buds with bill. he wants waters in there so when he calls passing plays he looks good.
--practice (running) at practice sams is at a serious disadvantage to show what makes him great. it's two hand touch on the quarterbacks every single practice as well as during scrimmages. in qb runs / options it's a lot easier for him to just get touched, and waters isn't that slow so he runs with no fear of getting hit and probably looks halfway decent at running the ball during practice.
--practice (passing) i think we all know waters has the edge in the passing game. but what about a passing play where sams ends up scrambling? well the play is immediately called dead and the coaches might even be a little upset with him because he didn't go through his progressions correctly or something. in the game that's an exciting 10 yard gain, in practice the play is dead as he jogs five yards past the line of scrimmage.