The only problem I see with using the eidolon concept (haven't looked over your specific iteration of it, yet) is that the eidolon is a much more powerful beast than the animal companion. I looked into this on a project of mine (since abandoned, sadly) where I was trying to make a cavalier/summoner multi-class valid using one combined mount/eidolon creature instead of two. Just looking at the advancement table the eidolon is at least four levels more powerful than the animal companion and that doesn't even consider application of evolutions.
You may have to be more specific on what makes the eidolon that much more powerful (besides evolutions) to an animal companion. A quick glance at the two tables reveals this (E - eidolon, ACo - animal companion):
HD - E starts at 1HD, max 15; ACo starts at 2 HD, max 16 (advantage AC)
BAB - E good progression, max +15; ACo medium progression, max +12 (advantage AC)
Saves - both E and ACo have 2 good saves and one bad one (push)
Skills - E starts at 4, max 60; ACo starts at 2 max 16 (advantage E)
Feats - E starts at 1, max 8; ACo starts at 1 max 8 (push, although ACo maxes out one level earlier than E and E can use feats ACo cannot)
Nat. Armor Bonus - E starts at +0, max +16; ACo starts at +0, max +12 (advantage E, esp since it doesn't HAVE to be put in Nat. Armor)
Str/Dex Bonus - E starts at 0, max +8; ACo starts at +0, max +6 (advantage E)
Evolution Pool, Max Attacks - No equivalent for ACo, advantage E albeit a big one
Special - E gains Darkvision, Evasion and Improved Evasion (1 level earlier) over the ACo; ACo gains 1 extra ability increase over E (advantage E)
AC "wins" - HD, BAB
E "wins" - Skills, Armor bonus, Str/Dex bonus, Special
Push - Feats (sorta), Saves
The eidolon def gets more than the AC, but I think this will be a good exercise in determining the size of a plant's evolution pool since the animals that you can draw with the animal companion have abilities of their own (similar to evolutions, but less powerful).
Not that this invalidates your argument, I think it IS cause for consideration into the size of the plant companion's evolution pool...maybe even something akin to the rate at which tricks are awarded for ACs. Also the amount and type of evolutions that are even possible could be adjusted.
Good thing to consider, thanks.