Two separate, but somewhat connected points, here. (Want to be clear, because just because you don't like point #2 doesn't mean you need to completely dismiss point #1...
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One thing I was thinking about was that Fallout 3 is meant to be a very long game (at least potentially so.) With all the DLC coming out to increase the play time, it's possible to be playing this game for quite some time with the same character. I think really, the most important consideration for the next Fallout (beyond most other considerations) would be a system that allows nearly unlimited character advancement. It doesn't really matter what the end goal would be, or the exact manner that was achieved - just that a player would be able to keep playing the game without hitting some sort of arbitrary cieling for their character. This doesn't mean it shouldn't be possible to get very good at every single thing in the game, just that I think for a game like this - ideally there should always be the possibility of just getting that much better. Even if after a time the bonuses become incrementally insignificant.
Point two, is an idea I'll throw out there on how to achieve this. A bit of a departure from both versions of the SPECIAL system, but still staying in-line with the sort of gameplay Fallout 3 is trying to do. The thing is, since it's a skill-based game, and it's meant to be played for a long time - why even bother with having levels in the first place? As you play, you'd just gain experience points that go into a communal pool, and when you rest at a bed you have a chance to spend those points. XP could go to either skill points or for buying new perks as the player wants. If you raise the skill cap and add lots of perks to choose from - you get both an effectively unlimited character advancement; as well as the freedom of it being impossible to "gimp" your character. If you don't like the direction your character has gone, you can simply continue earning XP until you can afford the perks you want.
Along that line - we could possibly just remove Attributes as well. Just replace any benefits you'd gain from Attribute levels with more perks. That means more options to select for customization, for one - as well as more perks to choose from. You could make everything a perk, essentially (except for skills.) If you want more hitpoints - there's a perk for that. If you want more Action Points, there'd be perks for that. That way, if you want a character with a certain degree of strengths and accompanying weaknesses, you could have that. If you wanted a character that's more generalized, you can do that as well. It would be up to the player at that point. Higher "level" perks would just cost more XP points, and possibly some would certain prerequisites.
The biggest hurdle I can think of would be an intuitive way to both display all the character's perks (since now you'll be ending up with tons of them,) their effects, and ways to filter through all the options when deciding what to pick. I can't picture what the character sheet would look like, in a way to comprehensively and intuitively show all that information. As well as being simple enough for a "casual" player to understand without being overwhelmed. But I'd see that as more of a challenge than an insurmountable obstacle.
It would be quite a departure in some ways from both types of Fallout games, but I think it might actually fit well with the sort of gameplay Fallout offers, without really drastically changing the way things work.