Altered Ego's ETB doesn't trigger any of your on-casts, making it not as good a choice for this deck as it seems. It can't copy Conduit well since by the time you cast it you can hit any of your drops anyway, nor Ulamog and Kozilek, and on World Breaker it's just a 5/7 reach devoid since the other abilities aren't active when the copy from Ego is on the battlefield. I'd cut it entirely for your fourth Offshoot: you can run sideboard Clip Wings to deal with Ormendahl, or at best play it in the sideboard.

As for what to replace it with, you're mainly missing a way to deal with Company and Aggro, and especially to pressure planeswalkers like Gideon, Ally and Nissa, Voice which can end to swinging through with 15 power of tokens just a turn or 2 before you hit your big eldrazi (turn 6 ish). A smart player of the token decks will anthem rather than flipping to Ormendahl once they see ego, because you run no wrath effects. Since both your main and sideboard are keyed towards going bigger than midrange and sticking harder than control. As such, I suggest cutting a Hedron Archive as well for 4x Sylvan Advocate in the mainboard. They dodge Languish on turn 4 given your ramp, pressure planeswalkers (without tapping), and prevent early attacks via 2 power in a way your Jaddi Offshoot cannot. Additionally, they are still good in the late game, as a 4/5 vigilance is almost always worth one draw. Lastly, I'd run at least 1 other variety of counterspell mainboard (any 3-mana will do) instead of 4 of one that can be played around like clash of wills can.

The last card I'd suggest is Nissa, Vastwood Seer  ^Flip. Given that Borderland Ranger was good enough to see play in its time, and your ability to flip her on turn 5 or so, and how much you like both her ETB and her flip 1 (it's better than Kiora's, closer in power to her -2 and Nissa costs less though hits later), it's a definite strong addition. Given your land requirement, Find a Forest = Draw a Card, and if you find yourself already mana flooded, cutting 1 land and 1 other card for 2 of those Nissas is reasonable. They are just too strong via card advantage, at worst an early blocker, at best a game-winning planeswalker.

It always sucks to see that your starting-card idea (ego) isn't as good as your shell, but I think that's true in this case.

Sorry about the slow response: Tappedout was crashing every time I tried to post for whatever reason. Now I'm going to try to split the post in two incase it was just too large.

I definitely agree about the trouble with pressuring planeswalkers against GW tokens. I've currently been trying out a version of the deck that uses 1 plains, 1 swamp, 1 mountain along with 4 Skyrider Elf to try and take the walkers out early (4/4 flyer on turn 3 ruins the days of Nissa, Voice of Zendikar and Gideon, Ally of Zendikar). Since that wasn't consistent enough, I'll be doing what you suggested and bringing in sylvan advocate (albeit only 3 of them) and sending the Altered Ego to the sideboard. With this change it's also probably worth bringing in a third Lumbering Falls in place of a Crumbling Vestige

(continued)

Again this one is too big so I'll have to triple post here.

For Altered Ego, while I agree that it sucks that I don't get the on cast triggers, having a scaling threat that can just be a 4 mana 5/7 reach if necessary, or in the case of Conduit of Ruin, a 2 mana 5/5 with a great effect. The sideboard should be better for it - to bring in against any form of control deck or any deck with Kalitas, Traitor of Ghet.

I had considered Nissa, Vastwood Seer  ^Flip but had no idea what I would take out for it - any suggestions?

Aaaaand finally:

Clash of Wills has consistently been and continues to be easily one of the best cards in the deck. Since it hasn't been seeing any play anywhere else, nobody sees it coming, and in the late game I have enough mana that it doesn't matter if they do. If necessary, it can go out for either Horribly Awry or Negate which are in the sideboard, but often I'll keep them in. Being able to use the +1 of my Kiora, Master of the Depths to counter my opponents turn 3 play is normally enough to win the game on the spot.

I'll admit I didn't see the synergy between Kiora - Deathcap - 2-mana counterspell. That is definitely something that makes Clash more reasonable. With respect to removes for Nissa, I recommend Hedron Archive. While it cuts into your ramp, you're already playing 38 mana sources without them, which is definitely enough, and Conduit of Ruin takes care of getting quickly from 6-7, where your other ramp gets you naturally, to 10. The archive's crack ability allows it to have utility late game, but so does Nissa, and the 2/2 blocker on turn 3 followed by a 4/4 blocker on turn 5-6 and guarenteed card draw every turn seems stronger. It also allows you to keep 2 lands - Explosive vegetation in a way Hedron Archive doesn't, and your 4-drop is already fuller than your 3 with your only 3 being pilgrimage and the "3-mana-skip" from deathcap, compared to kiora, vegegation, any mainboard ego's, and the "4-mana-skip" from Nissa's Pilgrimage. I'd run 1 archive, 2 Nissa instead.

That definitely sounds reasonable, and I agree about having an imbalance of 4 drops. I'll test Nissa, Vastwood Seer  ^Flip out and see how it goes. However, since I really like being able to go Hedron Archive into another 3 or 4 drop (effective mana cost of 2), and often run out of forests anyway, I'll play on in the place of Hedron Archive and one in the place of Nissa's Pilgrimage. Thanks for all the support :)