My system doesn't necessarily give you the best 25, but it should give you the best 53. That's what I'm shooting for.
I agree you should be shooting for the best 53. But you are only replacing starters in one or two rounds. If there is a guard that is better than NEP second best guard, NEP is better off drafting him than upgrading Hoyer in round 2.
Once we are past the point of drafting guys who could start. We start doing analysis of which would help the team more....adding this WR and dropping our 5th best WR or adding this RB and dropping our 4th best RB or adding this linebacker and dropping our 7th best linebacker or adding this QB and dropping our current backup QB.
This is the way to build the best 53, IMHO.