There may be a simpler approach to making the defense-nemesis prevent the player from winning with just the champion and minions, without making a near-stalemate inevitable for no-superweapons-other-than-champions game: make the defense-nemesis intensity decrease as AIP goes up.
Specifically, +AIP wouldn't remove any nemesis units but it would cut down the amount that it respawns up to. So maybe if AIP < 30, then you get the max, from 30 to <50 you get 80%, the normal, from 50 to <70 you get 60%, and so on, until only one nemesis respawns after a wipe. Or perhaps the amount of nemesis spawns is similar but the "recharge time" goes up as AIP goes up and (in theory) the AI is putting its resources more into the strategic reserve, special forces, waves, etc.
That way, if you want, you can build a huge champion, and then get AIP up enough to divert the AI's forces away from its champion-counter, and then kill it with the champion, but in the meantime you've had to deal with a real AI response instead of just the 10-AIP (or so) level.
Thoughts?