For me:
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Super Robot Wars (Gameboy)
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Berserk Millennium Falcon Arc: Chapter of the Holy Demon War (Mouthful, PS2)
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Gundam Battle Assault (PSX)
I love Super Robot Wars, it's the perfect you got peanut butter in my chocolate game. It mixes a dozen different giant mecha ips into a tactical roleplaying game.
Berserk on the ps2 is awesome. It takes the musou formula but imo makes it something much more engaging, plus it faithfully retells the best arc of the manga.
GBA is a great 2D fighter by natsume, carries on the tradition of the gundam wing game for the super famicom but this time on a 32bit system.
yeah, they're not gundam or fighting games, but they're still anime games that i loved, so into the list it comes ^^