I get what you're saying, that's a big concern for me too, but this guy's idea was to have 1 HOF and 3 gold. So if you want a 7'3 player that has HOF posterizer and gold ankle breaker and other badges that don't fit a 7'3 player, then have at it, because they'll probably suck at what they should be good at.
I saw this idea in another thread. Maybe this one! But perhaps in this system, the kind of badge you get to pick is limited to how high your attribute is, and depending on your player type/position, getting something to a high level that typically doesn't belong to that player should be costly.
For example:
Make a 7'3 340 center. You can choose to level up ball handling, but it will cost way more for you to max out than other types. Or a 6'2 guard having a high block rating. So if you decide you want to specialize in these things, then your traditional attributes (Like rebounding on a center or shooting on a guard) will take a pretty big hit.
Hanzsomehanz beat me to the punch!