So with dropping CHA to 1, your character, will be ungodly good.
In 2, you can do the same. You can just chew on mentants if you want companions, but again, you will become ungodly good.
Unless you want to nerf yourself, none of these games are hard, and special does not break a character. And it shouldn't, otherwise there would be only one SPECIAL way to win.
But see, the things you point out do not make FO3 a bad game.
And turn based...meh. And I love turn based. Now, I would like to see a Tactics 2 strat game that was turn based. But, I don't mibd real time, vats, or first person.
Not to mention I'm tired of the WC. Game stays on WC it will just be more and more of same factions growing, shrinking, growing.
But a lot of this is what you want improved. I also wouldn't be surprised if 3 had more quests than 1 or 2. Not to mention there is not too much to the quests...many of them are extremely easy.
A lot you list is cosmetic or mechanics. That can all be addressed, but I take the small settlements of 3 because people left, not wanting to live in a craphole. The people who do stay and try to make it work, well they got guts, or crap for brains.