I generally don't like flashers in any game. Here's what I do:
1) Turn the flasher brightness to the minimum in the menu
2) For LED flashers, I apply a Sharpie to all but a few LEDs. (I learned this trick from Melissa at Cointaker.)
3) Yellow LEDs are generally very dim. I use yellow LED flashers where possible.
4) Blue LEDs can be very harsh on the eyes. I generally replace them with white flashers and let the lens do the coloring.
I realize you are describing a design problem, but I hope this can help you enjoy your game better.