I'm pretty sure had this been an NFL game they would've alotted a longer development time and some of the more ummmm...
interesting stuff they did with APF would've never made it into the game. But whether it meant that the lack of polish would've been rectified is anybodies guess. After all, Tiburon's been making Madden all gen and that game lacks all kinds of polish so it's hard to tell what the outcome would've been. I see some polish issues with the 2K Sports games this generation that have kinda been at least partially eye-brow raising although not exactly game killing.
About the comparisons... It's a tough thing because on one end when you consider how weak Madden's been you kinda want to be able to have the 2K game come in and knock it silly. But then on the other hand you know deep down that comparing a game that's been developed every year of the generation (Madden) is going to be ahead in a number of ways over one that hasn't (2K Football). We're in a really weird place right now, lol.
I really expected APF (and now looking back probably unfairly) to pick up where 2K5 left off. Some say it did, I don't myself because I don't get the same feeling playing APF as I still do playing 2K5... and I like to play with created teams a lot on 2K5
(My Arizona Vipers cannot be stopped) so you know it's not just the NFL thing for me!