One think which is annoying me from time to time, is when the coach waited to the last minute to take his whole timeouts which make the most exciting part of the game quite boring(especially when the lead change and the other coach starts to take their timeout's too).
http://www.nba.com/analysis/rules_5.html?nav=ArticleList Chapter VII
So why not use the NBA rules for timeout rules, especially rule a which mean:
- only 3 Timeouts left, at the beginning of the last quarter
- max. 2 Timeouts in the last 2 minutes
If it is still planned, to implement "commercials" during the TO you also could include the rule that there had to be a given amount of Timeouts during a quarter or it come to an "commercial" break(VII.d) when you raise the incentive for the coaches to take them early without really bad series it maybe become a more natural flow into the game.
But i think at least rule "a" could be implemented easily, and will make the game more attractive rule "d" got more difficult and would just be funny when it ain't always the mandatory timeouts ;)