Wingflier, I understand what the game is set up as right now, mechanically. My argument is that I think it would be more interesting if the mechanics were different. As Darloth observed, the tradeoff between neutering one AI and pissing off the other. The game is about strategic level tradeoffs, and right now there just isn't a tradeoff when it comes to when you take out the homeworld. The only way to play (good strategy wise) is to take out both homeworlds as quickly as possible. At that macro level, there isn't a decision to make.
Of course, there is a lot of strategy involved in how you take out the AI homeworlds, but I think adding another high level would be interesting. I think it might also introduce some interesting scenarios that result from one AI hw being vulnerable long before the second is. For example, I'm currently playing a Maze A map, but one AI hw is located along the main path, and the second is something like 30 hops behind that one. If there was a mechanic where by taking out that first hw weakend one of the AIs in some way, it would introduce a tradeoff, do I go for the vulnerable AI now to weaken it, knowing that the second AI will get more aggressive, or do I wait until I can take them both.
On the point of the avenger plot, I personally have never found it to matter much. I'll grant that this is only the case because I always play with fallen spire and go for the fleet, so compared to stuff in the Exo waves a single avenger spawning isn't that dangerous. With a different set of options, the Avenger is more of a threat, granted. However, it is not a feature that adds, in my mind, the same strategic depth, it's just one more thing to kill.
I also personally believe that from a lore perspective it makes sense. In many instances throughout the game, various references are made to how important the AI home command centers are to their operations. Now if Keith decides that the lore is "two command centers means redundancy, so you have to kill both to have an effect" then that's what it is, but I think it would fit in with what has been established in the game to have it worked the way I've described.
At this point I'm just trying to generate discussion on the idea because I think it might be interesting. We'll see where things go from here.