OK so we need to cut 54 cards, except that you've got 18 lands, so you probably need to cut another 20 cards to make room for basics, so about 74 cards. 


Birds of Paradise, all the Signets, Abzan Banner, Chromatic Lantern--I don't love mana dorks most of the time in EDH because they die too much. Rocks are better, but if you have green, Rampant Growth effects are still usually better. I'm leaving Gyre Sage because if it's ever going to be good, it should be here. Commander's Sphere is super great.
Avatar of the Resolute--is just a big dude. Eh.
Den Protector, Renegade Krasis, Twilight Drover, Retribution of the Ancients, Condemn--These are just the least-good versions of things you have too many of.
Abrupt Decay--not great in EDH.
Black Sun's Zenith--not sure this is the deck for this card. You'll kill all your tokens (probably), but it will take a lot of mana to kill other people's fatties. Kirtar's Wrath might be worth a look.
Journey to Eternity--mostly I imagine you're sacrificing tokens, so they won't come back.
Necroplasm--unless you can put a counter on it immediately, it destroys all tokens at the end of the first turn you control it. Seems too risky.
Rishkar, Peema Renegade, Cytoplast Root-Kin, Fungal Behemoth, Mer-Ek Nightblade, Forgotten Ancient, Scale Blessing, Spore Swarm, Thallid Omnivore, Ivorytusk Fortress, Splitting Slime, Realm Seekers, Verdant Confluence, Gladeheart Cavalry--these just all seem to cost too much for what they do.
Path to Exile, Utter End, Vindicate, Sundering Growth--you have too much spot removal. Sundering Growth is on theme, but it's just going to make a single saproling, which seems maybe not good enough.
Beseech the Queen, Blood Artist, Zulaport Cutthroat, Poison-Tip Archer--you said you wanted to go less in a combo direction, so I suggest cutting some combo pieces and tutors. 
Ant Queen--turns mana into creatures, which is cool, but probably not as good at doing that as Ghave is most of the time.


Well, that's a start, at least. Some thoughts:


I love Thallids and very much want them to be good. Mostly they are not good. You may consider cutting them depending on how competitive you want the deck to be. 


You have way too many 3-drops right now but nothing jumps out at me as particularly deserving of a cut. But this is the most overpopulated spot on the curve right now.


There is probably too much ramp right now, but I'm not sure exactly how much to leave in.


You may want to consider cutting a lot of the +1/+1 counter support and focusing on things that help you make mana, make tokens, and draw cards. I think a lot of the time you win, it will be with an infinite combo, and the size of your saprolings won't really matter. Stuff like Hardened Scales and Cathars' Crusade helps you combo and synergizes like crazy with Ghave, but stuff that just puts counters on the team is less strong. But if piles of counters is super fun for you, that can be made to work, too.


You should be playing Skullclamp.