The old Fallouts were actually somewhat like what Fallout 3 did. Like UnDeCafIndeed said - they were levelled by zone, so that if you wandered into the wrong area, you'd find things were pretty tough, but once you'd levelled up enough you could walk right through certain areas without a scratch. I generally prefer this sort of thing over the "everything levels with you" thing they did in Oblivion. Because when it's done that way, I never feel like I'm getting ahead.
In Oblivion, for example, I tried being a thief-type, going for long-range sneak attacks as often as possible. But it never proved that effective of a tactic, because no matter how much I raised my Bow skill, or how awesome my bow and arrows got, I still couldn't make more than the occasional one-hit kill. (Which is the entire point of spending the extra time staying hidden and lurking through dungeons.) And since I was focusing so much on those skills, it took me a really long time to increase my melee skills enough to the point where I was able to deal with the enemies that I had barely damaged with my bow and had to deal with in a more convential way (which was most of the time, unless I could get myself up to a location where they couldn't reach me - a la the Arena...)
But like I said, for me it's less about the challenge, and more about just feeling like I'm always advancing. Fallout 3, for instance, even on the hardest difficulty level I didn't find I died any more often than on Normal - it just took me longer to get through the enemies. (And before people start defending it - I am aware that Fallout 1 and 2 were guilty of this to the same extent, as well. Though those games were more unforgiving in general - I died a lot on normal; and I died a lot on hard, as well.)
To bring this a little bit more on topic - what I liked about Fallout 2 was that there was really no need for a level cap (I think it was like 99 or something - basically you were never going to hit a brick wall.) And skills went up to 300. It's worth noting that these are just numbers. What I liked about Fallout 2 wasn't that my character could be 3 times better at Small Guns than I could in Fallout 3, but that I always had areas I could keep improving on.
The easiest fix I can see to the level cap problem you have in Fallout 3, would simply be to triple the skill cap. That way there's always skills I can spend points on. And it offers even more customizability, as well. If I wanted to have 100 in every skill, being a jack of all trades, I could do that. And if I wanted to be more focused in a few areas, I would be free to do that, as well. Plus, you wouldn't have to worry about the level cap at all - especially if like in Fallout 1 and 2, skills past 100 cost double points.
That's the main problem I found I had in Fallout 3. The first time through, I wasn't thinking ahead at all. I figured those Skill Boost Perks were something that would come in really useful, so I picked a bunch of those in the beginning of the game - as well as the Perks that increased my skill points. I was still in "old Fallout" mode, and was trying to make a very specialized character that made up for a lack of combat ability with the supplementary skills. But by level 20, I had run out of options. I had long since maxed out the skills I actually used, and was putting points into skills like Big Guns, which I never once used. I just needed to put those points somewhere.
My second time through, I actually had to min/max more than I normally would, just so that I didn't end up with a min/maxed character at the end. Sure, I had an 8 in INT, and I raised it up to 9 and then just by exploring found the Bobblehead without really looking for it. But I was roleplaying an Intelligent character - a lower INT wouldn't have made sense. (Besides, it would have ruled out my coming across the INT speech options, which was sort of the whole point in the first place.)
It didn't "ruin" the game, and I still had fun both times, but it's still not what I would have thought as ideal.
To emphasize, though. I think that simply raising the skill cap would give more options. The level cap is really just there because after a certain level you're guaranteed to run out of places to spend skill points. With higher skill caps, the level cap becomes irrelevant. And this seems to be a common complaint about Fallout 3 - people like gaining levels. And I doubt most of them want more levels just so that they can max out that last skill. It's simply that advancement in itself is a fun part of an RPG. It's the "carrot" that leads you through the game. You partake in side missions for their own sake, but also for the extra encouragement of getting some reward for your troubles. It's not the only reason, but it's a reason, in and of itself. And 300 in Small Guns need not be so completely overpowered, either. Again, it's just numbers. 300 could mean whatever you want it to mean - you just have to rebalance the game to take those extra skill levels into account. Not to mention that the work required to get a full 300 in a skill probably ought to be rewarded by making you needlessly deadly with that skill...