I would like to say I'm all about the role-playing, but that wouldn't be entirely true. It forms the basis of my choice but the decision also depends on the sort of character I'm playing. I'm more likely to go with a big and tough animal companion if I'm playing a character that isn't big and tough (like a spell-focused druid or an archer ranger) and, likewise, if I'm playing a tougher character who can hold his own in melee (like a shapeshifting-focused druid or a melee ranger) I generally go with a lighter, swifter companion.
I don't like the idea of trading off animal companions over time, however, as it seems to go against the very concept of animal companions. "You're no longer useful to me, Guenhwyvar. I've decided to trade you in for a dire elk." Yes, I understand the idea of allowing an animal companion to return to nature and live out it's natural life, but repeating this every few levels seems a little difficult to fathom. Particularly when there is no unifying theme and the player has a prepared chart as to which companion he/she will take based on his/her level.