I use a lot of my pets for missions and consequently I have a lot of leveled up pets that I don't really like any more hanging around. I don't want to get rid of them because they're higher level, and because it seems like the appearance of the pet is a more important factor in its pricing. I also notice that it seems random whether a lower priced or higher priced pet will have high or low stats. Is appearance/traits generally the most determining factor?

Say I hypothetically breed a pet that doesn't look great, but has amazing stats, would that affect how much it would generally go for?

Yeah, looks are more popular in pricing, but exceptional stats can get good gold as well, but usually if they're REALLY good.
The max stats a pet can have is...
1000 HP
120 MP
100 of all the other stats

If you can get a pet that has good base stats like 520 HP and 40ish other stats, it might be worth something.

Just wanted to note, the max base health stat a pet can have is actually 2000, not 1000.

Stat breeding is rising in popularity, not sure if that will effect the price or not, but a pet with at least nearly maxed stats are pretty pricey.

Oops... xD Did I get the other stats right at least?

//facepalm