I'd like to look at it with a wider and more metacontextual lens. Ethan had to use Blood Honey to introduce an almost entirely new audience to his characters while still attempting to make something reminiscent of his 90s work. More importantly, he had to build up as much interest in CyberFrog (the character) as humanly possible to make this crowdfunding venture last. So I would say that keeping CyberFrog out of a large portion of the story wouldn't be much of an option for Ethan, even if it would make for a better impact if we were to consider the story as its own entity.
Ideally, I'd have kept the parts of Blood Honey set in the 1990s about the same in order to establish the characters and show the initial Vyzpzz invasion to see what the enemy is capable of. After that, I'd have set a good stretch of the series in the post-apocalypse without CyberFrog. We need to establish the survivor colony and see them at their lowest point so that you can feel the weight of CyberFrog's return (or at least what it means to Heather). We would also get a better sense of how the new world works and how CyberFrog's interference is actually going to throw a wrench into the new establishment, given that he's now a vestige of the past and only knows 1990s Philadelphia. However, this story structure would only work under one of two conditions, as far as I can see it:
A.) If issues were coming out at a faster rate. Were this a monthly title, the audience could bear to go several issues without seeing the titular character if the writer was doing a great job of fleshing out the supporting cast and building the world.
B.) If 90s CyberFrog was an absolute smash hit that everybody read. That way we'd all be anticipating the return of a character we loved in the past and it would hit like an emotional freight train when we saw him again. However, this still leaves new readers in the dust. In this situation, Ethan would've had to put out Warts And All prior to Blood Honey in order to catch people up and start building their investments in the character (and the franchise, financially speaking).
Given that neither of these is the case, I understand why Ethan is doing things the way that he is. He needs to put as much *CyberFrog* into each issue as possible. The character has become an icon and it's what people want to see. He can pump out ancillary material with Heather, Lily, Salamandroid, etc., but the main issues have to be Frog-focused for the time being. I love the idea of an issue set on the Vyzpzz planet, though.
All that being said, I think Ethan mostly knows what he's doing and the overall story should be pretty solid when it's all said and done. The book being primarily from CyberFrog's perspective still works fine, as this way we will get to experience the new world in real time as CyberFrog does. It should make for a better 'fish out of water' feel, if Ethan does it right. Shouldn't be that hard when your main character is already a cybernetic swamp creature.