I kind of like the usage tiering system (does that make me weird?). Obviously it isn't great that a 0.1 point difference in usage can make a player much less useful, but it adjusts for the fact that top-tier usage guys (Jordan, Kobe, etc) are able to get their offense even if you don't have other scorers on the court with them at any certain time (not over the course of the whole game, necessarily, though, due to the individual penalty).
If we were using 100% total usage as the baseline to avoid a penalty and you had Jordan with 33.3% usage and Pippen with 24.4% usage (like on the 96 Bulls) you'd need the other 3 guys to have 42.3% usage or 14.1% each in order to avoid a penalty. I know it isn't asking much from a player to have that usage rate, but I'm fairly confident Jordan + Pippen could run an efficient offense with any three other players (as long as at least one of those players could provide some spacing, but spacing is a separate issue in the sim). And if you set the required usage rate to avoid a penalty to be lower than 100%, you'd run into the problem that owners would only draft for 90% usage or whatever you set as the floor (which would be equally unrealistic).
So, long story short, what I'm saying is that I like the fact that there are two separate factors at work - a kind of "do you have an epic level scorer on the court? if so, you're okay. If not, do you have two guys who can create their own offense? then you're okay. If neither of these, I hope you have five well-balanced scorers out there". My only suggestion would be that it could incorporate assists into the tiering structure somehow (i.e. Steve Nash doesn't have a high usage rate, but having him on the floor should help offset the team penalty more than having some awkward big man on the court who has a similar usage rate to him).