4 suggestions off the top of my head I have not heard mentioned:
Stop the clock after every first down made while the chain gang advances then re-spots the sticks...same as college.
Widen the hash marks on the field to their original distance apart, i.e. the same as college still is & the NFL used to be. The obvious advantage here is that there would be fewer opportunities for the incompetent zebras to mis-spot the ball placement.
Lengthen the legal chuck distance from a minimum of 5 yards to a maximum of 10, depending on the yards needed for a first down: if between 0-5 yards, the legal chuck distance remains at 5; if between 5-10 yards, the legal distance becomes the same as the YTG; and if > 10 yards the distance is capped at 10.
And regarding coaches' challenges, they should be determined by the number of timeouts a team has remaining: e.g., if you still have all 3 timeouts, then you should have At Least 3 challenges to use if you so choose; and while a team should Not lose a challenge opportunity (or a timeout) if their preceding challenge was successful, they would lose a timeout (and thus have one fewer challenge opportunity) if a subsequent challenge is unsuccessful.