After replaying several RTS games the one thing I Hate is population caps in single player modes. I understand it's for balance purposes but when your pop cap is as low as 50 or 100 and most units cost 2-4 points then that number rises pretty quickly.
I absolutely hate it when the creators of RTS games use 'balance' as an excuse for population caps (we know the real reason is because they don't want the games to drop frames from too many units being on the map at once; any other excuse they try to make is superfluous). If there is an issue with balance, it isn't because of how many units can be on the map at once. It's because the stats of units themselves aren't balanced well.
So for me, there are two things that I absolutely hate. The first is escort missions, where you have to babysit an inept idiot who feels the need to run face first into every ambush on the map, instead of waiting for you to clear everything out. Seriously, there is no way from any kind of real world standpoint that an escortee would do something that stupid, unless they were completely insane to begin with.
The second thing I've grown to hate is time limits. Now I know time limits used to be very prolific in games back in the 80s and 90s. But they really are a product of a bygone era and have no practical place in modern games. The challenge has gone from getting somewhere on time to completing the mission itself. In this day and age, the mission itself should be the challenge, not a gimmick like a time limit. That goes double for role playing games. If you need to have a time limit to beat an RPG that you made (and it doesn't involve some kind of school simulation), YOU'RE DOING SOMETHING WRONG! The ONLY exception is if you're using the time limit for an escape sequence, because the dungeon or area you're in is about to explode. And even in those cases, the use of it is still going to be brief and very limited in the game.