i found the 3.5 system a better system at the time because I loved the interconnected rules, and easy tables.
3E's great merit is its unparalleled robustness. I think this is what you're describing when you talk about "interconnectedness" of the rules.
The example I always use is Grappling. It's 1,600 words (2.5 pages in any other RPG book, but the D&D3 PHB has incredibly high words per page for just this reason) in the D&D3 PHB.
It's a lot of detail just to grab someone. When you read it, it all makes sense. Each step in the process makes sense, it works in a manner that is consistent with how the rest of the game works, and has a lot of detail. Robust.
If you like that kind of thing, then D&D3 is for you. I spent, no joke, 6 hours once creating a Bugbear boss (named BITER) who was a Lasher. A bugbear who used a whip. It took me six hours to make that one dude because there was no e-support, nothing like the Monster Builder for 4E. I had to go figure out how Whips work, Whip Daggers, make a whip attack that doesn't do subdual damage, does a whip attack provoke, all the various feats that let someone use a whip to disarm you, how disarm WORKS, a feat that let you pull the disarmed weapon toward you WITH your whip, another feat that let's you GRAB the weapon you just pulled toward you. The Lasher prestige class, what classes did a bugbear need to qualify, how many class levels did I have to give him to get the feats necessary.
It took six hours for a few reasons.
1: I did not have a high degree of experience with disarming. It's very complex in D&D3, lots of feats that cover it. D&D3 is built on the premise that overall, you always suck at everything and are unlikely to succeed at a grab or a disarm or anything like that, unless you take a few feats to become competent. So I had to learn a lot about how Disarming works and how you can become really good at it. If I wanted to play by the rules--and if I didn't, why am I playing an incredibly robust system?--I had to do a lot of research. Disarm and how Whips work.
2: All these rules were spread out over several books. There was a phenomenal amount of cross-referencing.
3: Once I knew how everything worked, and had all the books open to the right pages, it still took a lot of brainpower to create the character. Figure out how all the pieces fit together, try different builds to see what worked. It was not easy.
In the end, this monster lived about 8 rounds, which was about 90 minutes. And at the end of that 90 minutes I was delighted because Biter scared the crap out of my players and lived long enough to do all the cool stuff he could do, without me having to cheat to keep him alive. At one point the PC cleric summoned a Celestial Black Bear and sent him after Biter dismissively, "oh I'll have the bear take care of him" and the bear provoked an attack, and Biter obliterated him and everyone went "O_O".
But afterwards, happy though I was, I was forced to conclude that a 6 hour investment for a 90 minute payoff, on one NPC who I'd likely never use again (because how often can you get away with a Bugbear Lasher?) was a kind of madness. I spent longer on Biter than we did playing that night.
That's just me. I was in many ways the target audience for 4E. I was crazy in love with 3 and played it weekly for its entire history, but in the end I was desperate for something that didn't require so much work.
Last week I, as a player, watched as our GM, on the fly, using a laptop, the Combat Manager (indispensable, cannot imagine running a game the old way) and the Monster Builder, build an entire Kobold encounter on the fly, but make a custom Kobold War Drummer and Kobold Standard Bearer in seconds. Prep time? 0 prep time. No prep time. He did it on the fly, at the table, while the rest of us were roleplaying.
So if you want that kind of "I am an arcane researcher with my tomes open before me and guttering candles illuminating my vision," if you like that feeling of incredible depth in the rules and that pouring over them for 4 hours will give you a more optimized character than someone who only poured over them for 3, then D&D3 is for you. For many years, I was that guy. This is no indictment of D&D3, it made a lot of people happy for a long time.