My favorite part of 3.5 Edition was hands down the prestige classes. They were a way to specialize your character and help forge it into exactly what you thought it should be. Towards the end of the edition, they were reaching, but for the most part, there were a lot of cool options to be found for prestige classes. With the qualification requirements and everything, it just felt like prestige classes were a major way to define your character and what they were about. Don't get me wrong, you should be able to show what your character is without ten levels of prestige class just by playing the game and making choices while role-playing, but I felt like prestige classes were a very nifty way to mechanical way to represent your character and what they were about.
Feat and Skills kind of go along with prestige classes, I thought they were great ways to bring your character, via game mechanics, closer to being what you envisioned in your mind. Your fighter didn't have to depend on Strength or Dexterity to determine whether or not he hit hard or was hard to hit, you could take Power Attack or Dodge or Combat Expertise. I dunno, it just felt like between feats, skill points, and prestige classes, it was easy as Hell to make your character into what you wanted to be.
Challenge ratings were another concept I really liked, every monster had a challenge rating and in the DMG there were tables for building encounters and awarding experience based on the party's level and the challenge rating of monsters and traps and such you put in the encounter with them. It was somewhat tricky at times, and I don't think I fully understood it at times, but it made building encounters of the difficulty I wanted a lot more easier. It kind of just gave me some guidelines for building encounters that eliminated a lot of the guess work. I'm not a huge fan of taking a stab into the dark and hoping things work out.
Level adjustments and templates were pretty cool, a nice and easy system for indicating how powerful a race or template was and how much more powerful than other players that the race or template was going to be. It kept the power level of the players fairly balanced so no one was surging ahead of the group for most of the campaign, unless they had like a +4 level adjustment and some racial hit dice, then thing admittedly got a little crazy.
The d20 mechanic. Pretty much everything came down to a d20 roll, whether it be initiative, attack rolls, or saving throws. I liked that. It made the rules a lot easier to explain to new players and a lot easier to adjudicate situations not covered by the extensive rules of the game. You want to do something? Roll a d20 and apply pertinent modifiers.
Ascending attack rolls and AC and so on. High was good, low was bad. This kind of ties in with the d20 mechanic, but this made the edition glorious. Don't get me wrong, I had the THAC0 tables for each class pretty much memorized by the time we stopped playing 2nd Edition AD&D, but positives always equaling good and negatives always being bad was a great addition to the game I thought. It made it easier to explain to new players and it made combat a little easier as we didn't constantly have to reference attack roll sheets.
Ultimately, I think it was the complexity and wealth of options of 3.5 that made it appeal to me so much. This however eventually left a sour taste in my mouth with the advent of the 160 page splatbook for 35 dollars that was produced on a pretty much monthly basis. There is such a thing as too many options and too much of a good thing. Complete Arcane, Complete Mage, Adventurer, Scoundrel, Divine, Champion, etc, etc, etc. Spoiler alert, none of these books were complete anything. They just kept coming, never once creeping up above the 160 page mark.