To be fair, Force Commander lets you take some of your units to the next battle. It still doesn’t change the fact that Force Commander sucks.
I hate that control method, its a bit rubbish, probably why it was taken out of circulation. I love Goldeneye on the N64, finally a console game came close to the keyboard/mouse combo for PCs 
Yes, it sounds counter-intuitive, but when you play other games from a third-person perspective, such as Grand Theft Auto: San Andreas or any sort of 3-D platformer (e.g., Ratchet and Clank), it makes sense. And switching between a FPS controlled the way you prefer and a third-person game is confusing because my brain isn’t wired that way.
“Drop Quests” (AKA “Collection Quests”), mainly seen in MMPORGs, and the most vile ones I can think of occur in World of Warcraft. Particularly those in which the item you’re supposed to retrieve is something that every creature you kill should probably have, and yet mysteriously only one in five or one in ten of them drops it. The most heinous offender in this arena is the “Murloc Head.” Apparenly, only about one in five murlocs actually has a frigging HEAD. Similar issues with collecting the ears of various creatures (MAYBE one ear per creature, if you’re lucky) and the stingers from scorpions and related creatures. Sure, they can sting you, but that doesn’t mean they have stingers!
And, of course, there IS something worse than either an escort quest or a timed quest … I’m referring to the TIMED ESCORT QUEST!!! All the fun of an escort quest, with the bonus of failing because the damn unit you’re escorting goes off on a tangent somewhere.
Wandering Targets. Freelancer had missions in which you were required to go to a certain waypoint and kill or capture someone. But when wounded, those villains would sometimes try to, you know, flee. If you let them go, you fail. If you give chase, you start getting warned about “leaving the combat zone” and if you don’t return to the combat zone within 60 seconds, you fail. Nice mission design, that.
Indestructible Allies. I’m looking at YOU, Call of Duty 2! Somehow, while other NPCs are dropping like flies around me, Sergeant Voiceover and Captain Cutscene can be shot to ribbons and still pull through.
Regarding the “lose all your weapons at some point” gripe, Half-Life 2 does a great version of this, where the enemy ATTEMPTS to disintegrate all your weapons, but actually transforms the grav gun into some unholy engine of destruction with which you get to gleefully kick the crap out of the rest of the game.
Best. Weapon. Ever. 
I haven’t been reading this thread, because I don’t play enough video games to really hate things in them.
I was addicted to some 360 degree shoot and run in an alien asteroid kill all the machines you can game back in the 80’s — but I had to take drammamine to play it – made me want to hurl the spinning combined with the poor graphic horizon. Fun as hell, so I gues I don’t really hate it.
Currently I play only City of Heroes/City of Villains, but I’m thinking of quitting for several reasons:
1.) no travel powers – you basically run around and they send you all over the friggin’ place I estimate at some point in the first 14 levels you spend about 65-70% of game time going from point A to point B and back again. This is especially annoying when you run for 15 minutes only to be told oh, run over here.
2.) I hear a lot of people praise the story arcs, but if they were skeleton’s they’d be malnourished. They are not so much storylines as they are ideas for storylines.
So, that doesn’t save it.
Nonetheless, the coolness of being a super-hero does seem to trump all the bad stuff, so far.
This is one of many reasons I gave up on everquest.
The first game did this too. Your allies have three modes:
1.)Cannon Fodder: Most of your allies fit into this catagory and it’s particulary evident durying the Soviet Campaign. Don’t bother making friends with any of your buddies because almost all of them will die in the next few minutes, and might be replaced by a similar generically named ally who has just has much personality and chance of survival.
2.) Indestructible: Sgt. Moody is one of these guys. He’s pretty much invincible for the entire game, unless he’s…
2.)Temporarly mortal: If there’s something Sgt. Moody desperatly needs to do, he’ll become mortal just long enough for you to protect him.