Well it's an interesting concept, but one thing that absolutely needs to be changed is the way you move atoms around. My clicker finger was beginning ache by level 2, which is never a good sign. Instead of needing to click twice for every swap, it would be preferable to drag the atom through the grid, swapping with every atom it gets dragged through. Much quicker and less tedious that way.
I think what really kills the game is the audio. Aside from the fact that the pirate music is atrocious and the ninjas sound like creepy little gremlins, the music fades in and out for no reason that I can comprehend.
I crashed right before I passed the finish line. I was forced to continue into the endless void forever and ever, with no hope of escape (well, except restarting).
Each resource location (Forest, Cave, etc.) should have its own separate grid, unaffected by the other grids. Each resource location should only yield one type of resource. As matches are made, the number of matchable tiles decreases, but slowly replenishes over time. Let the player manually switch between locations, instead of letting it happen automatically after a set period of time.
Place the tower defense window on the left, and the resource collection window on the right, and allow players to directly control Trey with the WASD keys while collecting resources with the mouse.
Instead of the moving rows and columns puzzle you have for resource collection right now, change it to a "click clusters of 3 or more" puzzle; that way, you don't have to put so much attention into resource collecting.
I beat level 12 by first maxing out my size, then getting infected with a virus and going to town on the enemy cells, never splitting, always making sure to eat enough to stay big. It's like taking advantage of a superpowered evil side, with all the benefits and risks.
It's fun, but it's not very immersive graphics-wise. I think you should continue to update the graphics of this game, one texture or particle effect at a time, until it becomes a full acid-trip simulator. Until then, a 4/5 from me (I am a very stingy voter. Less than 8% of all games I ever play here are worthy enough for 4 stars from me; even fewer 5.)
I'm very grateful for your 4/5, believe me, and for your honesty - I will work on the graphics, but I need to be careful it doesn't become too overbearing or detract from the simple nature of the game. Thanks again!
This game would have held my interest past the BotD if the dungeon layouts didn't repeat so damn often. What is there to motivate me to continue, if I've apparently explored all there is to explore after only 15 minutes of play? Even with the huge number of characters to unlock, only a tiny handful of them are actually useful and worth playing. There might be some amazing characters or unique dungeons at the farthest edges of the world map, but none of that matters if I'm not willing to traverse the Hanna-Barbera inspired expanse in between.
Could I please bring my progress over from the official site / my Facebook account? I don't want to have to do the time challenges all over again to get the badges.
I completely failed at the second to last puzzle. It took me forever to finally realize that, in addition to clearing away red walls, I could click their outlines to bring them back.
It would be nice if up to four unfinished levels were available at any one time. Basically, 3 "skips" that would let you move on to a later level if the current one was frustrating you too much.
 "Brick Squasher 2"){kind=icon}
 "The Alchemist by Fupa"){kind=icon}
 "Bob the Robber"){kind=icon}
 "Pirates Vs Ninjas"){kind=icon}
 "Neon Race"){kind=icon}
 "The LaCoGeSSta Research"){kind=icon}
 "Glissaria"){kind=icon}
 "Pike Club Platinum"){kind=icon}
 "Microbe Kombat"){kind=icon}
 "Saving the Company"){kind=icon}
 "Accelerator"){kind=icon}
 "Ultimate Sonic Flash"){kind=icon}
 "Great Dungeon in the Sky"){kind=icon}
 "The End"){kind=icon}
 "ClickPLAY! Rainbow"){kind=icon}
 "Linx: Hard Set"){kind=icon}
 "Control"){kind=icon}
 "BioGems"){kind=icon}
I'm very grateful for your 4/5, believe me, and for your honesty - I will work on the graphics, but I need to be careful it doesn't become too overbearing or detract from the simple nature of the game. Thanks again!