If the AI really cared about you, it would just swarm you with 20,000 ships from all its planets and would kill you immediately. The AI's motives and where its attention lies has been discussed at length elsewhere. Suffice it to say, story in an RTS game for me is vastly secondary, and even having the AI always appear as intelligent as possible is secondary. What is primary for me is having game mechanics that are interesting and that provide a fun and good play experience. The AI is in support of that, not the other way around. If something is a semantic argument, providing a cosmetic or theme-based shift at the expense of gameplay, I'll always choose gameplay. Sometimes that bugs people, which is unfortunate, but I think it does a service to the game itself and mostly that is appreciated by most people most of the time.
It's not that I'm unwilling to make a change here -- but so far nothing has been suggested that provides an equal-to or superior gameplay experience while addressing the concern you have, so therefore I'm not going to make a change yet. If there's something that someone has that meets the criteria of making the gameplay just as good or better, then I'm all ears -- players often surprise me with sideways solutions I've never thought of. But I put quite a lot of thought into this mechanic back when I was originally designing it, and I haven't yet come up with anything that's superior.
Hope that makes sense.
Whenever I destroyed a warpgate I could say to myself "They can't attack me now because the AI can't warp 2 hops and traveling would take too long". Now that I know the real mechanics and that the AI can bypass the warpgate limitation anyway, it suddenly translates into "They can't attack me now because the game developer made it that way. Period".
If that's the way you choose to see it, there's not much I can say to that. But I think it's pretty clear that the AI prefers to warp its fleets directly into your planets; and only when it can't, it warps into its own planets and then uses conventional propulsion to attack you. There are disadvantages for the AI in doing this, by the way -- its ships tend to get more spread out, it's at risk of being attacked along the way, it gives you more time to prepare, and it has a less ideal way of exiting the wormholes to deal with Lightning Turrets/Electric Shuttles. I understand that you perceive this to be a major discrepancy in how the AI thinks, but I don't see it the same way.