If I'm honest, FO3 and FO:NV can simply be described as this: Good games, let down by a desperate need of an engine change. Plus, the MQ isn't really that big a part in the grand scheme of Fallout. I've barely started it, only just started working for Mr House. But plots need to be better, certainly, they seem rather lacking. The beginnings of FO3 and FO:NV were both "chase Mr. X to X location" which, although it got you a few locations and started you off exploring, is really quite boring.
I'd agree and go a step further, remove objective markers. How can you really consider it exploring if you have a spot in the middle of map that follows the individual or object you're looking for. A little extreme I understand but it seems it would make the game seem more adventurous and less...walk from point a to point b and shoot. Beyond that, imagine just getting rid of the entire skill point distribution system and base it off of use experience. The more you shoot, the better you get, the more you walk, the faster you move, the more you hack, the easier it becomes. They can make a truly epic and immersive game if they stopped clinging to the level based skill concept and let it happen naturally. Just a personal opinion, I love the fallout series since day one, I even have vault boy tattooed on my arm, the worst thing they could really do at this point is revert back to Obliv.....I mean Fallout 3.