Good attempt, but....
I admit to being a Mega Man fan, and I enjoy this, but some technical things kinda spoilt it for me.
The controls were somewhat sluggish. I did take your warning about the backgrounds in mind, but it's the actual controls that took getting used to. My major gripe is the wall climbing for X and Zero: it's nearly impossible to scale the walls quickly without falling, so you need to take it slowly, and that costs valuable time. I also noticed a glitch with charging: when you scale the walls and charge, then fire, your shot somehow ends up at the top of the screen! I also noticed Bass charge too.
But, I like this concept. The competitive aspect of the MM games are somewhat lacking, and its nice to see a time-trial pop-up! Good presentation, and some good BGM music complements the action. I love the touch with X sticking his arm cannon out when charging.
A little more work on the technical aspects and you've got a real gem on your hands!