A few on my "pet peeve that they'll never address, and other people might not find as annoying" list:
- penalties for retaliation. Use the replay to see who the instigator of a scuffle is, instead of penalizing the guy who reacts to getting shoved from behind or whatever it may be.
- players signaling a penalty. So annoying to see the O and D lines pointing at each other when there is false start/offsides. Or jumping up from being tackled and signaling for a facemask. Either the ref saw it or they didn't. If you're trying to influence the ref to call a penalty they didn't see, throw the unsportsmanlike flag.
- Receivers signaling the first down. Should be a 5 yard penalty after the play is over. Make it a 15 yarder for a repeat offense, or if their team is down by 14 or more. (I don't mind the quick first down signal, it's the overly dramatic posing that's annoying.) Heck, apply this to any kind of muscle flex or dance when your team is down by a couple of scores.
(those last two are for fun, I don't expect anyone cares enough to really make those penalties.

)