I guess the reason I stick with 3.5 is that it strikes me as the most concrete, well-defined and well-structured system. (I don't own 3.0) To get an idea of what I mean, first read this blog post. If you have an issue with the blog post, it might be addressed in one of the comments or supplementary threads, but in any case, I don't intend to debate it here, and this isn't the thread for that, either; this is just the blog post I found that is the basis for how I view 3.5:
Calibrating your expectations
In short, the basic structure, framework, design, and math of the system models realism with a high degree of fidelity
for a gaming system. Afterwards, a whole bunch of things were added, some of which were just bad. The overall framework, the non-adventuring support, the general math is very good. I can make a quite competent 1st-level weapon and armour smith with just the Commoner class, or a true 1st-level expert with just the Expert class.
However, the rest of it unfortunately varies wildly in quality. For an arbitrary selection of examples:
True Strike. This spell alone renders Touch AC nearly irrelevant.
Binding.
Wall of Iron. If you do not think this is overpowered, calculate its economic impact.
Time Stop.
Imprisonment. Making any non-reach weapon a liability if you do get within melee range of a wizard, or many sorcerers.
A few notes about these, without regard for obviousness: First, they are all caster options. Second, they are all in core. Third, even if a non-caster can get access to them, they do so by paying money for options that casters get for free, and the casters can still buy cheaper magic items.
There's a beautiful game in there. But it's buried under layers of varying design quality, and good, bad and questionable design decisions.
I just wish more people published their house rules, because I'm not that enthused to roll my own.
As for Pathfinder, much like some others in this thread, I view it as published house rules; ones I don't view as being, overall, enough of an improvement to switch. In addition, the overall increase in power level of all classes is not something I greet with enthusiasm.
Edit: Fixed blog link. Apologies.