Well, then I suppose perhaps I disagree with the implementation more than consider it "wrong". If it's "Let Coach Decide" then I don't think I should be influencing his decision so strongly. At the very least, this should be explained in the game manual -- the other options seem to act in a more straightforward manner.
My concern is that in game #1 the AI seemed to do as good or better of a job than I usually do in setting my lineup. I interpret this as it being privy to more information than me (sublevels of skills, the actual effects of stamina, the particular usefulness of certain skills at certain positions, possibly even the opponent's skills...). The results in that game were quite good -- I achieved very high team ratings (for what those are worth) and beat a solid team. The results in game #2 were pathetic for obvious reasons and I will make sure never to do that again until/unless the system is changed to something more useful.
I think it would be a good thing if you could set a starting lineup and have intelligent substitutions. In the all-blank-lineup game #1, I think 4 or 5 different players logged minutes at SF for me. I can't do that with any of the substitution patterns besides Let Coach Decide, but I also might want to prioritize certain players for gameshape/training/matchup purposes by setting them as starters. That seems reasonable to me. It's the same as this "weighting" system you propose but less radical/imbalanced.
I guess this is somewhere between a bug and a suggestion depending on perspective.