I'm going to slightly disagree with part of this review.
I was also tempted to say that a puzzle game should be about figuring out the solution, not trying to execute it. I've said the same thing for lots of other people's games, because, well, usually its true. Puzzle games should be: about figuring out the solution (not executing it), they should have one answer (not multiple), should present all the information up front (not revealed as you progress through the puzzle) and in most cases not time-constrained (this sort of comes back into the point on figuring out the solution rather than executing it). This game essentially does none of that :P In general I find the words 'puzzle-platformer' should be treated with suspicion :P
But I feel like this game is a bit different, its not really a puzzle game, therefore those rules don't really apply. It has puzzle elements in terms of figuring out how you're going to get the ball to all the enemies in time and how you will plan out the multiple character's runs, but I think ultimately its a skill based platformer style game, with light puzzle aspects, in the vain of Super Meatboy, rather than a puzzle game.
Like Super Meatboy, it gives you the flexibility to create your own solution rather than presenting a puzzle with a correct answer, it's more freeform than a puzzle game. This is the only entry in the game jam I've played through twice because I wanted to see what other ways I could solve each level; whether I could do them in less throws/less time etc. That's also an indicator it's not a puzzle game, because in a puzzle game once you've beaten a level there is no point in going back, you've done the solution and know how its done.
All that being said, yeah, I agree with most other things you said; the first level of having clones is a bit tight time-wise for an introductory level (i did it on my 5th try with 0.5 seconds left, but that's probably still a bit hard for a level teaching a concept) , and it took me a bit of time to realise that the captured balls was used as a double jump (which was a bit of a eureka!/duh! moment for me :P ). A level system would have been great, it did have a quick retry system though...