If fatigue is going to become more important in HD then it would be very helpful to have some coaching controls over timeouts. In real life you lose one of your TOs if you don't use it in the 1st half, you could either use it to stop a run, rest, or set up the final shot of the half (just examples off the top of my head). Many, many more strategic examples exist, especially in the 2nd half I don't think they all need to be listed.
Also TV timeouts would make sense, because those are key strategic times to get players rested (i.e. sitting a guy w/ 6 min through the under 4 min TO to get fully rested for the final push). I don't watch/follow D2/D3 in real life so I have no idea if TV timeouts are fully NCAA-wide so that makes implementing this a potential issue.
Many of you have much better ideas than I do so maybe as a group we could explore the value of TOs and how they are used in HD.