I've played both a ton. I've had NBA 2k6 since release and play it quite a bit even to this day, College Hoops I got on Christmas but have already played a lot of it. I don't think I can say one game is better than the other but they are somewhat different. I play NBA 2k6 just to have a fun half-hour game on my franchise with my favorite team, then I usually just turn it off and play another game in a few days when I'm jonesing for some NBA action. Franchise doesn't hold my interest like it used to, sometimes I start new franchises but they'll only hold my interests for a few days at best. College Hoops really has me addicted with recruiting, building my team into a powerhouse and trying to get to another school, and the games are extremely intense and you can feel the meaning and the pressure of each one.
It is true that NBA 2k6 controls much tighter but I always just thought they made adjustments to CHoops to make it a little more sloppy like the college game really is. I'd say if you're looking to just play some random games here and there and want to do all the stuff NBA players do in a real game go with NBA. College Hoops seems deeper, theres a lot more to do than just play the games on the schedule. The actual games in CHoops are more scrappy and slower than they are in NBA, they require a lot more patience and team work to score as well as alot more focus to defend.