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Mobile Suit Gundam:
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Iron Blooded Orphans - Orphans employed by a PMC manage to seize control of the company and fight for themselves.
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The Witch from Mercury - Country bumpkin goes to fancy space school where students gain standing and settle their grievances in mecha duels. Also yuri.
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00 - A mysterious organization seeks to end all war on Earth by fighting with their fancy robots.
Note: While the Gundam IP is huge, the ones mentioned are spin-offs and can be watched separately of other Gundam series.
Other:
- 86 - The Republic fights against a mechanical empire using their own mechs which are totally autonomous and definitely not piloted by undesirables.