Okay, since I actually have a bit of time off from work..
Cell Stage: I agree with some of the points here about how placement and such matters with the parts, but.. It's kind of like Pac Man without the maze. While there is a bit of fun found in putting on the spikes and such, then hunting down cells three times your size, it just seems overly simple. It's too simpliistic. There's only six parts and you hunt down all six parts each time. It's just the least interesting to me in terms of execution and potential.
Creature Stage: I actually like this stage because this stage is where you define your creature. You start as a lump with legs, and eventually tune your critter in to what you want. Sure, impressing other creatures isn't nearly as fun as just killing them. But hey, it's kind of fun making a race of giant frogs that can jump forever with the most upgraded frog feet. Or bird men who can fly.
It would have been nice if they took a page from
RoboForge for the Creature Stage. If you have a maceball on a long tail, speed and reach are defined by the length of the tail for the maceball's strike. If you put spikes on the back of the creature, they shouldn't really have a charge value but a defensive value instead. Basically, they should have implimented a mechanics of design element to the creatures. It's kind of silly that I can hide parts under other parts just for the sake of having that ability without ruining the look of my creature.
Tribal Stage: I hate this stage the most. In order to get the blue badge out of it, you have to carefully balance killing tribes and allying with tribes. There's no "middle way" to go about things. It often involves balancing the killing with gifting and domesticating along with the musical concert allying. It also seems to cheat a bit when you're killing the other tribe. They go from losing half their tribe back to normal numbers pretty fast. Of course, if you do a quick attack, kill as many as you can, then raid their food.. You can eventually starve them out and have your way with them. At very least, you should be able to domesticate and trade animals for a middle ground route.
Civilization Stage: Okay, what's the difference between military and religious other than the animations? The religious units shoot some kind of happy beam or something which causes the enemy city to switch religions. But hey, it seems to do about the same as the bullets. They couldn't come up with something better than that? Something like setting up your city as holy cities so that people from other cities make pilgramages to your city which turns more people in the enemy cities towards your cause would have been better, kind of a reverse trade type situation.
Space Stage: Hey, it's basically a space trader CRPG type thing. You do things, you get experience, you gain abilities. But.. The quests are generic as hell from what I've seen. Sure, they're a bit better than most space traders because you can terraform and such. However, it's too limited. You can only establish three trade routes at a time regardless of what level of trader you are. It takes forever to buy out an empire because of that which is silly considering the galaxy is HUUUUUUUUUUUUGE. It should be three routes times your level of trader, so once you're level 5 in trade, you can buy up 15 systems at a time. In fact, nearly all the little skill thingies are like that. You can max yourself out, but you're still once ship with a few chums doing everything yourself with the speed, or lack thereof, of just being the only one in the galaxy doing anything. If you're the warmonger guy, you should be able to control other fleets and send them to attack a system for you.
It would also be nice if you could make drop ships for fighting. I'd much rather be able to drop off tanks as opposed to zapping cities with lasers until they surrender. Often times, you shoot a city, all your allies will shoot and destroy the city. Ugh.
Also, I have religious weapons on my space ship so why no religious conversion of colonies?
All stages: There seems to be a decided lack of taking things from one stage to another. So your creature is a frog, they don't seem to do jump attacks in tribal mode. If they can fly, they use flight when moving, but they never use things like that in combat. So you allied with a bunch of creatures in creature stage, where are they in tribal? No where. If you ally with them in tribal, where are they in Civilization and Space? Sure, there's no reason why the allies from creature stage would evolve, but you could start with domestic animals. I don't think it would be hard to implement something simple like that.
Bonuses to certain things based on how your creature is built would be nice. If they're spitters, bonuses to shooting bullets would be nice. If they can fly, faster planes would be nice. If they have natural armor, more hit points on vehicles. Just something you can notice based on how you made your creature.