This is a really cool idea! I feel like the gameplay gets a little repetitive after a while, so maybe some kind of cool powerups or random events could be added to keep things spicy.
I think the two greens are a little too close to each other in hue/value. It wasn't easy to tell at-a-glance which green a puzzle piece was. I suggest making one darker/brighter or changing the color so they are immediately distinguishable from each other.
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I absolutely agree with the colors. I built out the 7 colors for frenzy first, then cut it down for puzzle mode. So frenzy looks great, but then puzzle's colors doesn't look as good.
The gameplay is a sort of the same, but there is an escalation where it gets more intense as the towers naturally build up higher. But I don't think powerups or events are a good solution for this, unless you can come up with a pretty compelling reason they would be.