giantsfan3:
But I really prefer to maintain the bootloader so that I can upload sketches via USB.
You can easily put the bootloader back again if you need to...
But honestly, once you start using an ISP you'll wonder why anybody bothers with serial. It's difficult to go back.
giantsfan3:
Is there some modification of the delay time variable that can be done to the bootloader itself?
It has to wait in case some serial data arrives from the IDE, so...not really.