My two cents on the Neuron issue already mentioned: The entire problem would be fixed by either A. being able to transcend at any time but you don't get any bonus below the threshhold or B getting Morphogens earlier.
Also on the topic of transcending: The way this mechanic is implemented is like really really bad. It gets exponentially more expensive whilst always providing a 30% bonus that stacks ADDITIVELY. There is no incentive to transcend more than 2-3 times because of diminishing returns. It either has to stack multiplicatively or if you want to go a additive route it has to scale. So trancending with more Evocytes gives a higher bonus.
Otherwise I actually see quite a lot of potential if this game gets more fleshed out.