Base Upgrades

Pop Thorn Attack Damage Numbers

Tough and Puffed Upgrade Path

Controlled Breather Upgrade Path

For most players, especially rookies, I would suggest Tuff and Puffed.  I think most prefer the roll attacks you get with Rollerpuff and Prickly Body is a huge asset to counter mobs of enemies as it seeks out who hits you and delivers big hit points.

I myself perfer Controlled Breather.  Aero Trampoline is very hard hitting amplified and the biggest deal to me is Scattered Winds.  I'm a big fan of his gusts (ie while Popped), so this path makes sense to me.

If you also prefer his gusts and the speed Pop Thorn has while popped, take Controlled Breather.  If you prefer his Puff state and spike attacks take Tough and Puffed.