GLaDOS gets Portal 2 tech because she doesn't have anything remotely close to offensive weapons in Portal 1, except Deadly Neurotoxin, which doesn't apply to bots. Round 3: Each AI has technology from their attendant canon (Skynet has T1 technology, GLaDOS has Portal 2 technology).
No gels are available for offensive use in the opposing facility (ie- moondust in the enemy AI core is out), however may be used as desired in base defense. Assume they are strong enough to do terminal damage to an AI core in a trivial amount of time if they get close enough. Since they are player-controlled in-game, assume Atlas and P-Body are at least as smart as a T-1000. Portals are available to both sides, but restricted to in-game limitations (Portal gun must be carried by a humanoid, two portals per gun, portals must be on a flat, stationary surface, etc).
Animal King turret is allowed, Party Escort Bot is not). Round 2: Both AIs are installed in Portal 2 tech level bases (Turrets, Atlas, P-Body, reconfigurable rooms, emancipation grids. Must have a significant biological component. Time travel is allowed for both sides, subject to the rules of the first movie. (T-800 (and lower) chassis with any trim (learning mode may be enabled or disabled at the AI's will), H-Ks, Aerials, automatic weapons, phased plasma rifles in a 40Watt range, etc) Portals do not apply here. Round 1: Both AIs are installed in Terminator 1 tech level bases. Let's say two weeks prep time because defensive tactics are heavy in this scenario. Directly remote controlling them, however, is not allowed. Combat / infiltration units may be programmed as desired by the AIs. Facilities are evenly matched in terms of manufacturing output volume so brute force / war of attrition is out. The core can, however, be protected by any available technologies. Assume the core is a single point of weakness and there is no redundancy or backups whatsoever (no, you don't need to destroy -all- of GLaDOS' cores). The goal is to infiltrate the other's facility and destroy the AI core. Assume planet earth is a wasteland and these two AI's and their attendant facilities are all that remains (Chell is dead, John Connor is dead, Wheatley is not a factor). Purely mechanical matchup no humans involved.