I am nowhere NEAR being an expert (or even good) at this, but I tend to look at the abilities. If they have something that benefits form going first, or last (say Spawn of Onyxia and its tail swipe), that helps me decide the value I put on speed.
It also depends on if the pet has healing abilities, and if those abilities are base on it's health pool or the dmg it does. Or, the composition/abilities of the team you plan to put that pet on.
I imagine, if you do PvP battles, a big part of it is also probably knowing what other pets are popular for people to be using, and knowing what breed is best to counter those, but I haven't PvPed yet.
Beyond that, for me, it's just kind of personal preference. I'm glad someone asked this, though. I look forward to reading responses form more seasoned battlers