So, hear me out:
The overall sentiment right now is... not that appreciative of the story. I'm right there with you, honestly.
In some ways, it's a compounded effect, built up over a long long time that has finally buckled under its own weight.
That brings me to this. While I don't think I could claim there's much fixing the story where we are, I'm wanting to entertain... a different course.
Hence, I think I'm going to engage in some speculation for where the story could have gone if it had chosen... alternative paths.
My rules will overall be simple for this thought experiment.
1) If you feel like contributing or arguing the premise, sure. Let's go with it.
2) Native walkers will appear, basically, where they did. They have reason enough to be there, what with being from there.
3) I'll only be tweaking the bits of the story revolving around where the walkers show up, since they bloody well drove so much of the story. To that end, there will be some alterations insofar as how I feel the story can be improved upon and where meta reasons dictate things like color balance, I will attempt to adhere to it, but it will first and foremost be about the story itself.
4) I'm going to slowly work on this, never doing more than focusing on one block at a time, possibly casting my attention slightly forward as if it were a formulative design team. In essence, I'll consider where walkers might want to end up, but I'm not planning total arcs for anybody since the butterfly effect is probably going to be in heavy effect.
5) I won't be changing block/set order. As best I can, I will stick to the structure the design team had laid out, but I'm going to prioritize characters where they make sense. If that means there will be unavoidable issues like the horrendous dragged out Chain Veil arc... not sure if there's much I can do about that when it happens.
6) If a detail becomes established, it stands. Even if wotc later decided that those details were... Inconvenient, it freaking stands. Retcons will bounce off. I'm looking at you, Origins.

As a side note, there are 2 blocks I intend to skip right out of the gate. Lorwyn introduced the planeswalker card type, but it... really didn't matter. Alara, meanwhile... I don't really have any complaints about how anybody showed up. I mean, Tezzeret's appearance is weirdly out of sync with everybody else, but... eh. Native walker.

So, the first block that I will attempt to alter will be Zendikar. It might be in a few hours, it might be in a few days, we'll just have to see how the treatment goes.

Alright! Time to begin in earnest.
I have already said that I didn't really see anything wrong with Alara and intend to leave it as is. (I mean, there were problems, but nothing that changing out any individuals would actually make a difference towards.)
That brings us to Zendikar.

Going to be upfront, from the very first moment we got any story on Zendikar, there had been one detail that absolutely boggled me and kinda pissed me off the entire time.
From a lore standpoint, the events of the Purifying Fire and the duel between Jace and Chandra over the Dragon Scroll had taken place 3 years before the, at that time, present day. Consequently, Jace's sudden interest in the event always was just... stupid. It was a minor assignment he undertook during his time with the Infinite Consortium and not anything that he really had any reason to look into after having basically blown up his life during the events of Agents of Artifice. While it is minorly implied that Bolas might have nudged him, even the big ass lizard himself admitted that it was a gamble, and that's just needlessly contrived. What’s more, the encounter he had IMMEDIATELY prior to him off galivanting to Zendikar is an 8ft tall barbarian busting in looking for his ex and choking the crap out of him. I would think THAT particular event would be more pressing for him to follow a lead on.

With that admission out of the way, that brings me then to the most substantial change involved with Zendikar: No Jace.
And while I'm at it, I'll do one more: No Sarkhan.

Now, I know that sounds like it's going to mess up the flow, but I assure you, it won't. Instead, we have one individual that can fulfill both roles from a meta perspective.
A blue walker that can act as an agent of Bolas and that has a specialty in colorless artifacts. What's more, it would still effectively be a plant for the Mirrodin block as a roadsign.
In case it hasn't become apparent, I mean Tezzeret.

In Sarkhan's stead, Tezzeret is sent to the Eye of Ugin to study the Hedrons and the artifacts that are holding the Eldrazi in place. Along then, comes Chandra, who has been searching for Zendikar since the events of Purifying Fire, and additionally, we get Gideon searching for Chandra, but instead of showing up late, he takes Jace's place in the initial conflict, giving us the requisite 3 walkers there to break the first lock.

As a purely Melvin note, Tezzeret, Chandra, and Gideon would appear in the first set, to align best with the actual story flow, Worldwake would feature Sorin, and then Nissa would finish out in Rise of the Eldrazi.

From a narrative perspective, using Tezzeret in place of Sarkhan and Jace both doesn’t really profoundly impact Jace’s journey at all at this stage, but Sarkhan, it most certainly does. To what full extent? That… remains to be seen. It will really depend on when next Sarkhan makes an appearance, but that will only be the case when we actually see him next.

As for Chandra and Gideon, putting them actually next to each other again and further removed from the events of the Purifying Fire, I think we can actually move up the time table on how they respond to one another. The biggest hiccup Gideon’s early appearance causes is that he doesn’t actually encounter any Eldrazi and kick off the rather tepid prologue to actually doing the Gatewatch. Otherwise, I could see it in his nature to just go back to check on things later since he was involved in the altercation to discover the issue at that time.

Then we come to how we deal with Tezzeret. At the moment in canon, Bolas was rebuilding him mentally, but we don’t really need THAT much lead time to say he got fixed. What’s more curious is what effect it might have had on him being in the caves. I don’t see it having the same deleterious effect it did on Sarkhan, but for him to be unaffected would be… boring. So, something to ponder on that.

Comments are open and any speculative direction anyone wants to provide is perfectly open to such things. Next step will be our layover to Mirrodin to see… it’s maybe not doing so hot.