And here I thought I was so clever, avoiding evolving until after I had completed the side-quest...
Personally, I think it was a missed opportunity for some extremely interesting endings. If you wanted to maintain a dyad of endings, I would suggest the following: 6A is overshadowed by 6B, not shaking up the formula, and evokes similar feelings as 1A, and 5A is also similar, being far less interesting than 5B. Since the player is assumed to have already mastered the combat in late-game (since they presumably have gotten all #A routes), the feeling of discovering the alternate endings for each path could be expanded upon further with doing things in an unexpected order (as much as the linearity of the game allows) and would keep interest while the endings are ground out for completion. I got bored grinding every ending because there isn't much strategy (you can just use proto-form for every fight except the last, then evolve rapidly to get your desired ending with the help of AeLOT biomass, which is quite dull.)
Otherwise, the game was highly engaging and entertaining, and manages to conceal its inspirations just long enough to maintain intrigue while still knowing what audience it cultivates. Highly recommend.
P.S Just a minor critique, but I think the final eye upgrade is a bit unimaginative, simply rehashing the previous tier's exciting change - perhaps invert the colors in addition to shifting hues, or some other filter?