I feel like the first two abilities are fine, but looking back I'm unsure if the third is underwhelming. At least I feel that colorwise I have her nailed on the head (flavorfully Lili only makes a brief appearance when requested by peer Rok-Byn).

I don't think you need to have only the creatures with +1/+1 counters on them be the ones that gains +1/+1 in the Ultimate. I know that there's a desire to tie it all together, but, with it, when this card ultimates it could kill two creatures and do nothing else. Like you said... not very impressive. At least if the bonus went to all your creatures, regardless of whether the second ability has been activated, it would feel more "Ultimate".
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Anyhow, while I appreciate Planeswalkers that read like a book, Planeswalkers that tell you what you should be doing can be unfun to play with. I think these cards work better when the -X is at odds with the ultimate.

Suggested templating: "Put two +1/+1 counters on each creature you control" (as per Stand Together and Ajani Goldmane), and "Destroy each creature with a -1/-1 counter on it. For each creature destroyed in this way, put a +1/+1 counter on each creature you control."

And that is now a nice Planeswalker. Nice ultimate, nice + ability, nice middle ability. I might perhaps suggest the first ability should say "on up to one target creature" as otherwise you can't level her up on an empty board, and it hurts to do so if the opponent has no creatures or their only creatures are hexproof or prot-black.

It does have the unfortunate trait that it'd be virtually impossible for Wizards to print with their current policies, because it deals with both -1/-1 and +1/+1 counters. But I've always thought that policy was slightly excessive anyway, so for a custom set this is fine.