I agree with the OP. I like open world games, but they can be pretty soulless. The best parts of Fallout 3 and NV are when you're surviving. Take that away and you're back to playing Oblivion again--lots of stuff happening, lots to nerd out on/collect, but the gameplay feels empty.
5 hours into AC2 and the number of fucking icons on the map just kept multiplying with shit you can do. I gave up because none of it was particularly interesting. I don't care about finding secrets when there's no danger and little reward--there are like 100+ of an object hidden everywhere, so it better be an easy task. If it were difficult, you'd have to have less of them and since there are less and you do want to make them a challenge, you have to craft them which takes time. Just put 100 feathers in the world instead! So, the difficulty is not in the finding, which is where it should be, but within your own will to subject yourself to the task. A couple mainline quests in and that seemed like the motto of the game-- the only thing that could get in the way of me succeeding at being awesome and hailed as god in AC's universe was if I stopped playing it
I think AC might be the worst offender. In bethesda games, there's some aspect or hook that really delivers. In Crackdown and inFamous and others, you run around the open world with super powers. Saint's Row is about letting the player be ridiculous and interact with the world in the most ridiculous ways possible. GTA is about crime and experiencing a ridiculously realized urban area. I guess AC is supposed to be about free running and assassinating, but the running is boring because there can't be any tension it--the game's hook is the ability to run around like that. And for a game with "Assassin's" in the title, they sure do play fast and loose with that word.