This deck has a lot of cool ideas, but it is a little bit all over the place. I think you can optimize it pretty quickly with a few changes and make it very strong.
For the combo plan - Arixmethes goes infinite with both
Freed from the Real and
Pemmin's Aura (infinite green mana) and a 1 card combo is a lot more efficient than the 3 card combo
Animation Module. I also think that
Deadeye Navigator is a great option for your
Cloud of Faeries and
Peregrine Drake infinite mana combo. I also think you need a way to win once you generate infinite mana. You can solve two problems at once by including X draw spells like
Stroke of Genius and
Pull from Tomorrow. Adding
Thassa's Oracle or
Jace, Wielder of Mysteries can give you an instant win after drawing your whole deck. Another good infinite mana combo for your deck is
Kinnan, Bonder Prodigy and
Basalt Monolith. Both cards are good in your deck anyway because you have a ton of permanent based ramp for Kinnan and it is an infinite mana sink.
Basalt Monolith is just good ramp that sometimes goes infinite.
For the non-combo plan: I think your instinct to cut out the +1/+1 counters theme is a good one. It doesn't really fit with what the rest of your deck is trying to do which is ramp and play big threats. If you really want to keep it, or even if you don't,
Hydroid Krasis and
Prime Speaker Zegana are really good card for your deck as a threats and card draw. Your commander gets you straight from 4 mana to 6 or 7 the next turn, so I think your threats should be around that mana.
Nyxbloom Ancient seems great for combining your mana doubling theme and your big mana theme. Just put in your favorite big creatures and have a blast.
Overall - I think you have a really fun deck on your hands, and you can optimize it with just a few changes. This is just a suggestion, and there really are a million different ways to go with Arixmethes so do whatever you think is the most fun. My last piece of advice would be to cut out a bunch of the tapped lands like
Simic Guildgate. You are a two color deck, so you shouldn't have a ton of trouble getting your colors especially with all of your ramp. Basics will make you a turn faster.
Have fun brewing up this deck. Best of luck.