first off, part of me died a little in sadness at the mention of Age of Empires. I miss playing that game.
Anyway, I don't think there is anyway a Sixais (controller) can be just as good as a keyboard and mouse. One of the reasons is the same that it may take a while for people to develop their own styles of play. I say this because unless you change around the buttons, there is no way you're going to be able to bunny hop and be effective with a controller since you'll have to take your thumb off the analog stick to press the button. It's a little off topic, but a controller is why I think the Orange Box is broken on consoles, I feel that TF2 is almost totally ruined.
As for bunny hopping itself. My problem with it depends on the game. I don't have a problem when it's used to try and throw somebody off from shooting them and it's a game mechanic (take TFC for example and just try to hit a bunny hopping/rocket jumping person with a sniper, it's quite the challenge). However, in a game like Battlefield 2, there is actually a bug or something that makes it hard to get any hits on somebody who is bunny hopping and I guess you could call that person an exploiter or something. Saying that bunny hopping isn't inteligent (in a game like UT3) sounds like the kid in Counter-Strike calling everybody a noob even though he has the lowest score.