I know this post has evolved beyond 3 players but this was a well thought out post. I'm sure the Bb's will keep tweaking the GE until some things are better and then everyone will complain about the next thing. We can make suggestions and hope, but the fact remains that this is the best Basketball Sim of its kind out there, hands down...
Obviously, the system could use some tweaks, but I don't think GS is one of the areas at all. Training and out-of-position is something else, and it would be nice to see some changes there.
As far as GS and competitive line-ups go, of course a weak team (div. IV) has no business in the cup at later staqes, but that's because it's a developing team and comparatively weak. The opposition would blow them out. And they could even do that by fielding their back-ups. Further on in the cup, as I said, it's a choice really - throw a regular home game and field your best for the cup, or not. Of course, there are those rich and established team that don't need to throw any game, but they represent fringe cases. And teams which don't suck and are on a level equal to you or me, we'll they're in the exact same boat. They also need to make choices and develop a strategy for the season. If BBs changed the way GS works, a cool part of actually coming up with a strategy for the course of the season would be lost. I wouldn't like that to happen.
Oh yeah, one other thing about minutes. I'm quite sure that with low stamina guys (3-4) it is much more likely they'll get about 36 minutes. I've rarely seen minutes closer to 40 happen on a consistent basis (since real battles to the very last second are also not that common). And 72 minutes in total isn't bad for low stamina guys, and higher stamina also enables playing more minutes with no adverse effect for GS (that was a really good tweak).
And there's another trick you could use, "sit them". If a team has a consistent fouler *and*a quite good bench player, this can be used to control minutes and game performance (of course, training becomes very problematic that way, two guy tops for one position regimes).