What do I miss? The freshness of Civ3. Coming off years of Civ2 /Test of Time, Civ3 was really something new.
A little OT: This was following 9/11, and on the same month my dad passed away unexpectedly, so it was a strange time, but I had Civ3 and it helped me through my grief. I had something to look forward to, and to play.
Back on topic - What struck me about the game was everything was new. There were now borders & culture and the AI understood it. The national treasury was where your income flowed through. Units were supported by your empire, not by your cities. There were even sort of interesting mechanics like AI governors who would sort-of remember what you were building and suggest things a long the same line, though Soren never got it to work properly, it was still an interesting thing to see.
The diplomacy was amazing coming from Civ2/TestofTime. The AI on large pangea games (16 AI all at once) was a thing, and it created some very interesting diplomatc/wold spanning results. The trade table was amazing and fresh. You could offer your own deals and almost everything had a price (later on, people found out how to make interest bearing loans and make arbitrage trades. ) I remember someone had found a bug in the unpatched vanilla game where if you beat down a Civ badly enough, you could get them to pay you increadible gpt (something like 500 gpt) even if they didn't have the income. The game was just printing money from thin air, but the strategy was called 'vassal strategy' and the word stuck, and it was discussed ad nauseum even after it was patched. People wanted something like vassals in Civ3.
I'd like to think that bug led directly to the Vassal system in Civ4, but that's really just conjecture on my part.
I miss that freshness. Civ5 had 1UPT, but the release version was so buggy, I spent most of my time angry *at the game* and defending it from the trolling it was getting. The game has certainly improved by leaps since, but I don't know if I'd ever experience the awe I did with Civ3 back in October of 2001.