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Wave canceling, while it sounds like an easy way to win, is not just "destroy the warps gates and rush to the AI Homeworld". It takes a lot of skill to use this properly, especially on higher difficulties. IF peopel decide to cheese it by making the wave warnings longer than default, that's their decision. You'll eventually have to deal with Wormhole invasions, which not only happen naturally like CPA's, but it gets extra budget added to it every time you cancel a wave.
https://wiki.arcengames.com/index.phptitle=AI_War_2:The_Era_of_Discovery#New_AI_.22Verb.22:_Wormhole_Invasions-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
"New AI "Verb": Wormhole Invasions
Add support for Wormhole Invasions. These are sudden Behind-Your-Lines assaults by the AI through Exogalactic Wormholes. They are intended to be scary, unpredictable and hard to defend against. They are also infrequent, and will not happen more often than once per hour.
The AI has a new budget type for Wormhole Invasions (to go with Waves, Reinforcements, etc). To spend that budget, it will spawn an indestructible Exogalactic Wormhole will appear on a player's planet. This wormhole is unstable and will disappear in a few minutes. The AI will launch a number of attacks through it. Sometimes it will launch lots of weaker attacks, other times fewer but larger attacks.
You will get a Notification while the Wormhole Invasion is active, but a minimal time warning when the attacks are actually coming (30 seconds currently).
The Wormhole Invasion will prefer weakly defended planets behind your front lines
Exogalactic Wormholes can also be used to spawn regular waves.
Wormhole Invasions are only available to the AI at Difficulty > 4, and it's gated behind AIP then (right now Difficulty 7 requires 160 AIP for the Invasions to start)."
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It makes sense as well. How can the AI launch waves if the warp gate they are going to use to teleport the wave into the galaxy is destroyed? That's like closing a door so someone can't get out of a room and then you turn around and they somehow are in the hallway.
Also, Warheads are not in the game yet. Well, they were, but they got taken out. So your concern about Warheads might have some merit, but that can be discussed later on with a Warhead balancing topic or something like that.
Your alternative has a few problems.
1. There are no transports at the moment. Guardians can store ships in them but the ships immediately exit when there is a hostile presence. Actual transports do not exist.
2. That is literally Exo waves from AIWC. We already have Exo waves. Once you scout the AI homeworld, the surprise is over. Not only that, the wave will give you the position of the homeworld. (unless it zig-zags all over the place) "Oh, the wave came from that way? The AI homeworld must be over there."
I also want to mention that cross planet waves are off by default. That means some noob isn't going to get destroyed by a normal wave showing up out of nowhere