You've touched on a few things that are somewhat true... I'd say it's about 75% who you draft and 25% how you play 'em. I've been shocked at some of the things I've seen people (good owners whom I have a lot of respect for) do or say about managing their teams. Mismanagement is probably the number one reason a lot of owners have 50-win teams when they should have 65-win teams. It's also a big part of when a #1 seed goes down to a #4. The biggest reason for that, though, is sim randomness.
But it's absolutely true what you said about cookie cutters. That's the nature of any stat-based sim, however. You need a certain amount of stuff do succeed, so you take and get the guys who get you the most stuff at the best price.
The things I'd like to see in the sim that aren't there is a better substitution logic system. This has been talked about for years with good, positive suggestions at how to attain it. But those suggestions have been ignored.
Many things that would add more strategy to the game would also add more subjectivity, and with the guys in charge of this thing, I don't want to see that. I'd rather they take what they had and work towards making it better before they add more things to screw it up.
PS - I don't know why people think you won't see Rodman anymore. His 93-94 season is the absolute best bargain in the sim now. There's no reason to use anyone else at the 4 (well, other than using a favorite player you can't put somewhere else).