If presented with statistics of game length in the NFL from before instant replay reached its pinnacle to pre-instant replay, I think we'd all be surprised to find that the length of the game did not increase drastically. In fact, instant replay, itself, seems to be getting more and more efficient as umpires and referees get used to the system. The biggest issues impacting the length of baseball games obviously rest with the media and the simple fact that there are no timers in the game of baseball. Sure sure, you can tell me that there's a 30 second time limit per pitch but have you actually seen that called in a major league game?
As far as the other two concerns about instant replay, it's safe to say that as technology increases and becomes more prevalent in society, fans are going to want it implemented in the game. Eventually it will be implemented, but if done properly by Bud Selig, it can be slowly added to leave baseball with that good ole "human factor". If he appointed a committee to compile a list of scenarios that could or could not be reviewed, that list might be exhaustingly long, but it would provide a good starting ground.
The NFL has provided a great example and precedent. While it may not be original for MLB to copy the NFL's system, it sure would help quiet all the noise surrounding controversial plays. Give each manager a red flag and let him choose when to challenge. You win your challenge, you earn a second one...it's as simple as that. The longer you wait to add further instant replay to the game, the longer you look foolish Bud Selig. Give the players, managers, umpires, and most importantly, the fans, what they want.