I've always been wondering, does Bowser have a more powerful or faster stiker shot? When you charge up with b, his meter is much smaller than other characters like luigis. It's harder to get it on orange. A few other captains have this as well. Anybody know?

No I don't believe so.

Faster captains have bigger green and orange line for the speed of the ball and strong kickers have bigger green and orange line for the amount of the balls.

Daisy and Waluigi have the hardest chance of getting more balls, but easiest shot at fast Megastrikes, making them pretty much the ones to go with if you're going to try a Megastrike.
Bowser and DK have terrible chances at high Megastrike speed, but they can more easily get more balls, which makes them a bad choice if you're going to rely on Megastrikes.
Megastrikes are a pretty desperate shot against a good player, though.