I can't say that I have much of a preference.
Maybe cherries, because of how the perfect cherries look in NL, but I'd be happy to have any of them otherwise.
I prefer eating strawberry because it's good in taste and also better for health. It contains nutritions which are really good for the physical health.
I liked the peaches at first because they're super pretty!, and in every single one of my Animal crossing games, I get apples omfg
but I'm thankful i got apples this time because the perfect apples look like candied apples, and I love those!
I could never get pears to grow in CF, so I was happy to have them as my fruit in NL! (But I dislike eating them IRL.) And being fond of gold, they're lovely!
When I get another copy of ACNL, I plan to either aim for peaches or cherries, because I love the idea of a town covered in pink blossoms come springtime, but...I really love how perfect peaches look! (I love perfect apples, too, but my brother gives me ones from his town even though I can't grow them - but I do set them in my houses haha.)
I'm also fond of lemons. (When I see lemons and cherries in my inventory, I always want a cherry lemonade...)
I like cherries the most, followed by peaches. Apples are okay and oranges and pears are nothing I would ever want. I lucked out and got peaches as my native fruit and three cherries from Isabelle. In WW, I had cherries as native fruit, so there's the sentimental value as well.
The first town I ever got had peaches and from then on, I disliked peaches. I don't know why.
But when I started playing New Leaf, I didn't care that much anymore. And I got peaches immediately... But I actually don't mind, because the Perfect Peach looks awesome!
Apples are my favourite, though.