Maybe beyond the scope of what you've asked for, but... Have you considered designing your own system? Or is that perhaps, anywhere down the road?
I don't think you said precisely what nagged you about D&D post-3.5 ... (And I really have no opinion on 3.5 either.) In other words: I wonder what exactly you are
trying to find in a system. I haven't done a lot with system games for years, myself... But I've found that when I do
at least think about running a story with some system (at least a small one), shaping my own miniature system can be a relief. Presumably you know what sort of genre and particular atmosphere you want to play, so you
have some idea what the mechanics should control and how they should feel when they are used.
For an example of what inspires me though, I would go back all the way to Top Secret SI. I think it was First Edition, though I've forgotten and maybe it was Second. I was in like, barely high school. Hee. Anyway, I loved
the derivation of various secondary character attributes each from two or three primary ones. I liked having a system that could do a lot with straight percentage rolls, including figuring crits right into the roll. I liked that it was an elegant
numbers system. No need for ten kinds of dice, or a hundred of them on the table -- pretty as they are. Who knows, maybe I even liked the brutal simplicity of the notion that each single toss of the dice could
be very important -- the system did not seem to demand
rolling all that often unless something "serious" was happening? And if you could think of other professional knowledge areas, you could probably add them (or build a story just around them, if you wanted) and convert them readily into success tests.
Twilight: 2000 (I had the 1st ed.) was another game that did much the same thing a couple years later, with a slightly different genre, more gear and some different "primary" stats oriented more toward a combat focus.
Many years later, I ran a PM game here with Mia Saisyu using an attributes test system based on that. Nothing to do with the espionage world envisioned in Top Secret or the postwar dystopia of Twilight... But a very similar mechanical foundation with very different character and narrative foci. It wasn't a very complex system
, per se. I had huge leeway to plot the difficulty of challenges and a range of possible outcomes; there was no campaign or creature "source book" purchased in advance with neat tables of what stock encounters might bring. But kinky and bizarre situations -- inside a computer adventure no less -- are what Mia wanted, and that meant envisioning things in slightly surreal arrangements. More generally speaking: I like to think there should be room for creative flex (even fudging the stats of the "plan" as you go) when designing something that is supposed to have both story and a kind of paced challenge. It's sometimes work but if you have enough adventure plan, it can be fun work and you may get more of what you came for.
I'm a little dubious about how far any one published system can fit so many particular people (or at least my particular story tastes), though. I too played some D&D once upon a time, and between finding players and working "around" the particulars of the system, it could be a hassle trying to get what you wanted out of most of the books. We did have quite a bit of fun, too. But I think most of it was when we focused on story/ adventure with only a few
key mechanics and then things moved so fast dramatically, we were usually happy to leave the rule books out of it.
Anyway, I hope you can find the kind
of system you like.