hm....havent played the gcn version in a while, to repeat everyone else the acres are definitely different. also theres no flower breeding/hybrids, you just plant them to look nice.
there's also the wishing well in the lowerish-center of town, which I don't think reappeared later. with it you could return items to villagers who had long moved away (like if you were sent on a task to deliver something), and a few other options.
ALSO!! you get tickets from purchasing items from nook, and at the end of each moth there is an auction where you spend the tickets to try and get rare items, many of which are emulators of old NES games. those were probably my favorite thing that didnt make a comeback (due to reselling these games in console shops on dsi/wii/etc)