Besides team practice time and playing time is there any other factors that effect how quickly a player will improve in learning a new offense/defense?  Some players on my team seem to pick up things faster than others are.....

Their High School GPA impacts how fast they learn things .. but you can't change that.

So college GPA has no impact? Seems like if a coach is willing to put minutes into study hall, and the player gets good grades, it should factor into improvemement. Just thinking out loud...

College gpa affects likelihood of need to add SH minutes in future seasons to avoid academic disqualification. HSGPA may still factor into that, but it isn't clear how much. To clear up a point from the OP, PT does not directly impact IQ improvement. Indirectly, by improving WE, PT improves IQ growth rate.

Rate of IQ growth is a function with HSGPA, WE & team practice minutes as the only variables. Well, maybe the multiple walk-on penalty applies, but I doubt that could be figured out unless the developers said as much. Some improvement occurs over time even at 0 practice. You'll notice that juco players will still have a F in unpracticed sets while upperclassmen will have some improvement even without practice.