The Ghost Recon games: I am an elite soldier, with the cutting edge of military tech at my disposal, and I am stopped by a damn chest-high wall! (at least in the PC versions)
Actually, ANY game where I control a single character (be it FPS, thirs person, or even one of those weird voxel type Diablo2-esque games) that doesn't allow me to jump or scale an obstacle. (Mass Effect being guilty of this, a LOT)
Fallout3, I can't disguise myself by wearing appropriate clothing. I.E. Even full sets such as power armor that hide EVERYTHING. And quite honestly, in all the big and wide Raider encampments, you'd think that I'd have a chance of stealthy approach by quietly snuffing some dude, maybe even from an another camp, taking his armor, changing clothes, using some mud. And voila! A few cuss words into my vocabulary, they'd just think I'm a raider from an another group, wanting to join.
I mean, I'm not even asking to be full fledged in their workings. Just as an added layer of "protection" they won't attack me unless I get REALLY close, or talk to them.
Also, despite what was told on the F3 game box, the story is linear, just has a lot of side quests and branches. What if I don't want to chase after my dad? What if I want to join the raiders. Maybe I'm good with meds, you'd think there'd be people out there who'd want a doctor. I mean, I am forced into going after Nielson. What keeps us going are quests, basically. Would it really be hard to create a quest generator, A-LA Face of Mankind? You have a set of objectives, completing a certain number of those will generate a new list, and the game keeps on going and going. Your daddy becoming a vague memory, a shadow in the past. That's be nice, if you ask me. Doing the main quest would have perks attached, like faster leveling, better loot, story, etc, but where's the replayability in that?