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I think it's random. When you change map choices in the beginning you get different fruits. I don't think it has to do with the order of the map choices, but if you don't like your town fruit, just don't save your town and start over :) I think when I did that a couple times my fruits were different. I can't remember really so I can't say for sure though. But I don't think it's tied to the cartridge at all.
Actually, I want pear trees. Since they won't be worth much, I'll cut most of them down and replace with apple, cherries, and lichees. Then I still make a ton of money and have plenty of my favorite fruits.
Currently playing: Harvest Moon: A New Beginning, Kid Icarus Uprising, and Animal Crossing Wild World.