Could be great if done properly.
The alien world is strange and exotic, full of alien environments. An entirely new world to explore. Full of ADVENTURE!
The alien empire is vast and multi-racial. There are actually multiple factions, species, factions, tributaries, vassals, all working together... Until you come along.
Humans have used tech to infiltrate alien defenses, rather than blasting things from orbit.
Due to being the invading forces, humans must deal with serious logistical issues. Imagine waiting a terran week for new agents to arrive.
Humans can infiltrate alien society (perhaps masquerading as the aliens' own human auxiliaries?) and then creating their own infiltration. Giving the subject species ideas of freedom and self-determination. Create resistance cells, hire alien mercenaries, freeing aliens from mind control, preach the religions of Earth to the godless alien masses.
Start stealing alien technologies, sabotaging alien industries, terrorizing alien cities, raiding alien colonies, pirating alien trade vessels, kidnapping alien civilians, and generally unleashing complete chaos and havok upon their society.
All payback for the horror they infringed upon the human race over eons. And BOY, does it feels good to hit back.
(If you want to play a moral ambiguity card, show how X-COM is becoming little better than the aliens)
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