V2 is great. I would like the option to zoom out the skill tree even more, but as far as it remembering its zoom, you fixed that.
I thought of an interesting idea that could be used to gain perks like not having to click—for example, hover attack. You could have special nodes that, if selected, cause a tower defense mini-game. There would be an obelisk with the perk on it in the center of the screen and mobs attacking the obelisk. The obelisk has a hit point value, and there is a timer; you want the obelisk to survive until the timer has expired.
I’m thinking of something else that might not have been done before: instead of allowing someone every perk in the tree, perhaps certain perks—like the hover attack, earthquake on spacebar, or others—are linked in such a way that if you win one of them, the others are ghosted out, including their entire branching trees.
That would give a reason to try different runs beyond the game's procedural generation.
A local and global leaderboard might be nice. If you do a global one, you’re going to need some way to prevent people from abusing it; I’ve seen global leaderboards hacked before.
And definitely a save system.