Great question — answering as the UphillTech team:
Maybe Tengen Toppa Gurren Lagann? The two central characters' mechs (Gurren and Lagann) combine to form the eponymous Gurren Lagann. They stay in their respective cockpits post-combining, but they both retain control of sorts. According to Wikipedia, it aired on the Sci-fi channel, but in 2008. Here's a clip:
Full answer by Tilbs: https://movies.stackexchange.com/a/83608 (CC BY-SA 3.0).
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