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Several thoughts. You need some ramp in this deck as most of your spells are heavy on the mana cost. Green is great at ramp so i would suggest you look there. Maybe Horizon Spellbomb or Cultivate or maybe Rampant Growth
Next thought Garruk Wildspeaker would fit well in this deck as he would add some mana ramp, and his ultimate is a great win con. Towards that end i would suggest another bit of wincon be added like Overrun or Overwhelming Stampede
Other thoughts if you can afford it then jace, the mind sculptor is pretty much an auto include in any blue deck.
I'll list here deveral cards that make your +1/+1 counters multiply insanely: Thrummingbird , Gilder Bairn , Contagion Engine , Fungal Behemoth , Protean Hydra , Primordial Hydra , Hunger of the Howlpack and Scute Mob . You could check my deck:golgarisimic-counter-generator deck for ideas
Ok, so there are multiple things that I think you can change here:
Remove the Helium Squirter s. They may give you flying, but they come out much too slow for a 3/3 graft. Instead, add in two more Aquastrand Spider s, they defend from flying since you really don't need it as much as your opponent does. Plus they're Grizzly Bears .
Simic Basilisk isn't that great. Sure, it gives your creatures deathtouch, but it doesn't really do anything else. Besides, a creature with enough 1/1 counters can defeat anything thrown its way. It's also really weak for its cost.
Simic Initiate seems like a good idea, in fact a lot of simic decks have 4 of him, but a deck with 2 Experiment Kraj needs some way to get mana other than your blue or green to take full advantage of his ability. In this way, it may be better to replace them with Birds of Paradise , which not only acts as a mana creature, but gives you any color you want, instead of just the lands in your deck, like Fertilid .
A better replacement for Overwhelming Stampede /Predatory Focus would be Mirrorweave . This card makes every creature a copy of target creature, which you can abuse by targeting a 0/0 grafter and making everything without counters 0/0, which makes all creatures without 1/1 counters die instantly. Use Simic Guildmage to move the counters to creatures without them.
The Vigean Hydropon looks like a good long-term investment, but Gilder Bairn is even more so. The Bairn has the same cost, can be cast if you don't have one of your colors, and can untap itself to double the counters on a permanent. It might seem like you need to attack with it just to double things - which might work if you are planning to make IT the grand attacker (move counter with Simic Guildmage or graft it) by doubling its own counters - but that's what Tumble Magnet is for.
More Cytoplast Manipulator s and Cytoplast Root-Kin are always welcome in Simic graft 1/1 counter decks. Manipulator takes control of creatures for cheap, while Root-Kin increases counters while coming out strong himself.
Some card draw is also really nice in decks like this, and Lorescale Coatl and Sage of Fables are so broken that it is quite a common find in such decks. These two creatures allow you to remove a counter from one, draw a card, and replace the counter. It becomes 2 mana draw a card, with no drawback. If you have multiple Lorescales, then removing a counter on one adds a counter on the other, which is a great way to power up your snakes.