I spent like an hour with an ai bot yesterday trying to figure this out... I randomly remembered playing this game and kinda want to try it. I'm fairly certain I played this on my windows me PC. In my search with the ai it recommended a lot of games, but none were it... Like not earth 2150, not a Gundam game (although it seemed heavily influenced), and not mechcommander. I think it was rts light as I generally loathe rts games but remember playing this game a lot on my old computer.
Some extra details. One big notable detail is the game was in little pop up windows. Like I could see and still interact with my PC as I played. It had mecha suites which were the strongest unit to build. They looked like the Gundam zaku units ...and I think they were red or blue depending. I would drag units to the other window and the suits and ships would fly to the other windows to try to destroy the enemy's base. The cut scenes were like cartoon ish pixel art things and if memory serves, the first major villain was the guy that trains you, but a bit into the campaign. Other things worth mentioning, I think I got it from Ollie's for super cheap... And I'm racking my brain to remember if it came bundled or solo...I generally would buy bundles back then (mom said I can get one game... Best try to get as many on one cdrom set).
Angryishhumanoid had the answer! Metal marines.