You can't rapid-fire because the shoot button already functions as a charged shot when held. I do agree though that remapping the secondary Jump or Shoot key on controller (for keyboard I think Shift would make the most sense) to be a continuous stream of uncharged shots would be a beneficial change. However, it would break the games' balancing if the player could auto-fire at anywhere near the rate of the Jet-Ski. Either it would need to be probably 1∕3 the rate of the Jet-Ski, or fire in 3 shot bursts. Have a feeling that 3 shot bursts would be a better fit in a few ways.
There's absolutely no chance that they add crouching or crawling to this. It's a pretty faithful implementation of the original couple Mega Man games' design philosophy, and just as Metroid can't crawl, Mega Man can't crouch