Assume that most of the rules for standard Canadian football remain, what would you change if players were not wearing pads (say a rugby uniform instead)? Note that this is less for TV games and stuff and more for amateur league play.
I'd change the following:
Force full, rugby-style tackles.
Limit unsafe blocking.
Limit blocking abilities on linemen.
Remove the ineligible reciever requirement.
Two field refs, two line judges.
Remove the tee.
Only make major obstruction a pass-interference call.
40-second play clock, 20-minute quarters (shut up I know it's rugby-esque)
18-man squads - force teams to play two-way ball.
This isn't necessarily all, but it is for now.