Both are pretty much tied as of right now!
How about this question:
Name one favorite game of yours from each series, and then compare those two.
City Folk and Animal Parade. I have to say that AP was clearly better because all City Folk had to offer was better graphics and a city. In AP you have marriage, dates, rival marriage.... it goes on. It even has an ending!
Harvest Moon: A Wonderful Life vs Animal Crossing GC;
Though ACGC is my all time favorite AC game, Harvest Moon AWL still beats it in my book, but only slightly. I've played the HM series since the very first SNES one, and I still own it, so that automatically puts it in a higher standard to me. But what HM lacks is a huge sense of connected community, and AC definitely has that. When playing AC I feel like my whole town is connected, and not just a bunch of people dotted around and keeping to themselves, like in HM.
But what AC lacks is all the other stuff that HM has, which is perfectly fine for their individual series. If I could add anything to AC, it would be more flowers. Not hybrids or color variations, I mean completely new flowers that also branch off into those hybrid and variations. HM could use a stronger knit community, have the neighbors talk to each other more often and not have the same dialogue every time you talk to them.