I got annoyed when I couldn't put stuff on the mantle of the fire place in City Folk :/ Some people like animal tracks and some don't. I think this issue could be resolved by giving the player the option to enable it or disable it. I personally don't like it because I never wanted to make paths anyway and I walked all over town watering my hybrids, so the grass was getting worn away everywhere.
The only other thing that I can think of that needs fixing is dialogue. The villagers need more lines. I rather enjoy talking to the villagers, at least I did until they started repeating themselves all the time. Oh, one more thing! The UFO. The freakin' UFO. Sure, Gulliver was too easy to get furniture from in the original, but the UFO in City Folk was way too hard. I don't think in all my months of playing I saw it even once. If they're going to do the UFO thing, at least make it so that it actually appears sometimes. I read online that it usually makes a weekly appearance, but it didn't seem like it.