The system used with Waters has been fairly successful, even the running game. I only really have two issues when looking at how he's been used; a) speed option is a terrible play for him to run and b) if anything he (or the backs) perhaps should be running more, especially on 1st/2nd down. Part of the problem he's had with 3 and outs when he's in is that he's asked to throw more often on 1st down, which sets up 2nd and long which never has been a great down/distance for Snyder (or any team). When Waters is off (which he goes through funks of being off, especially on quick throws toward the sidelines), that usually leads to 3rd and 10 and a punt.
I agree that Sams has to be allowed to throw more, but I think the passing game they have for him is far more limited than for Waters. Even on his two late picks against OSU and Baylor, he had pretty simply 2 level route reads (short and intermediate). Against OSU he made the incorrect read and threw the deep ball into double coverage, against Baylor it was more like the fortunate completion to Thompson last week; he got flushed from the pocket and tried to make a play and threw a bad ball. Generally when he takes the shorter routes to the sidelines he's in pretty good shape and completes them at a very high level. The deep ball he threw to Thompson last week was the same route that Waters missed in the 1st quarter, and then underthrew (but Thompson caught) on the drive previous to the Sams' throw.