I didn't read the whole thread, just skimmed a bit, but I didn't see anything addressing my biggest issues with FO3. So, I'll do that.
In general -not just in Fallout 3- I find that evil characters in most RPGs these days that let you be 'evil' tend to get shafted into being what I like to call 'The Reluctant Savior.' In FO3, you can ignore the MQ, but that's not really 'evil.' Okay, so you gave Dad the finger and walked the other way, then what? You've got no option to side with the Enclave (though there is an infuriating part where it
looks like it'll let you, but when you tell them what they want, they just kill you), you can't murder the BoS because their leader is 'Essential' (this Essential Character concept is another gripe I have with TES IV/FO3, but irrelevant at the moment. I'll get to that in a bit.), and ignoring the urgent facts won't let the Enclave take over. The game waits patiently for you to feel like saving the world.
I do not like this.
Sure, timed games are often equally maddening (sometimes moreso; anyone ever play
Pikmin?), but you should be able to tell the game, 'No, I don't
want to stop them, so quit waiting on me and just let them do their thing.' As it stands, you have to side with the 'good guys' (though you can have one last laugh at the end, but it doesn't matter for all that much in the long term), whether you like it or not. TES 4 (3, too, to a lesser extent) and Fable II did the same thing. You can be a jerk, maybe even downright evil in spots, but in the end, you gotta finish the fight for the good side if you want to finish it at all.
In Fallout 4, I'd like some options to be majorly evil. Sure, the whole Megaton thing was fun.. for a while. But there was nothing else big like that, was there? Raider factions remain eternally hostile with no chance to join them, I personally felt more like an outside contact in the Paradise Falls job rather than true part of the slaving operation, and [Broken Steel/MQ End spoiler]
Spoiler even if you do have that last laugh I mentioned before, they conveniently have the giant robot kill Eden so he can't give you the Enclave job you were promised anyway.
I felt like I was just allowed to be a pain in the ass. I wasn't evil, I was an annoyance.
Now, I'm not asking for them to make the main quest with fifty or so endings depending on what you do, but a little bit of consequence would be nice. If you're Very Evil, you can just toss around some Purified Water and all your sins are forgiven eventually. Nobody cares that you, y'know, murdered everyone in Megaton, Rivet City and all the killable people in the Citadel. Three days pass and it's all peachy. Though I might be annoyed by it at the time, I think it's a perfectly reasonable consequence that when you got through and kill a pile of people in a city, those who remain will shoot you on sight. Forever.
Which brings me back to Essential Characters. Though I know it's not Fallout related directly, I feel the need to point out that TES III: Morrowind allowed you a choice in the matter. If you
wanted to stab everyone in the world in the face, you
could. If you happened to stab someone in the face that was needed in the business of saving the world from Dagoth Ur, it would politely tap you on the shoulder and inform you that you've buggered up. If you find that you really don't care about that issue, you can continue play on in the 'doomed world you have created.' However, the fact is that when I take the time to rampage through a fortress of Power Armored soldiers, I would really rather not find that a few of them merely have an allergic reaction to the plasma I pumped into their skulls and pass out for a token amount of time. If nothing else, it kills immersion.
So.. that's my two caps on the matter, and my two biggest gripes about Fallout 3.
EDIT: Don't get me wrong though, I love the game, bought all the DLC and will buy any more they make. I just think those two things make it a little less enjoyable for those who prefer the life of a wasteland deviant.