The idea here is to ease canon junkies into the alternate universe that operates according to my beliefs. The canon still exists in-universe, just a different one. The benefit is that I can reference Starcraft lore.
With an eye towards constructive criticism: basing your AU on the most objectionable elements added by SC2 (the whole Xel'naga were actually extradimensional gods, rather than an advanced technological race with a bad uplift record) is probably a bad way to go about that.
SC is heavily character driven, even when that doesn't always make sense.
Your goal is basically StarCraft, but closer to the manual and where the characters and stories are playing out as small parts of a much larger scale, yes?
Then keep SC1 roughly intact. In particular: the fall of Tarsonis and Mengsk's betrayal of Raynor and Kerrigan; the Birth of the Queen of Blades and the invasion of Auir; the death of the Overmind at the hands of a small coalition of Protoss and Terran.
Part of the problem with the small theater focus you want is that the Protoss and Zerg are both large forces, particularly if you want to get into the Protoss Empire with client races and all that. The death of the Confederacy gives the Koprulu sector a reason to splinter and previously marginal/out of focus powers to rise. The fall of Auir gives a perfectly good reason for the Protoss to splinter. The Queen of Blades acts as a disruptive element in the Zerg harmony and the death of the Overmind gives the Zerg a reason to splinter.
There's plenty of room to play with recast characters and events in SC1 to bring those events about in a reasonable manner, particularly if you're trying to make it more faithful to the manual.
Another note: the more recent the element you want to change is, the easier.
You want to excise everything about SC2 Xel'naga, especially Amon? You will get cheers.
You want to radically change the board prior to the start of the first campaign
and massively change all the characters and their roles? Be prepared for people asking why this is SC at all.