I think the original question was, "If you had to be SPONSORED by one company," not "If you only could throw discs from one company." I would DEFINITELY go with an Innova sponsorship, but Innova lets their pros throw some Discmania and Millennium molds as well (so koda could keep his PD's). My bag is almost all Innova already except the Scorpius, which I could still throw with an Innova sponsorship, and the Fission Volt which I could replace with either a beat TeeBird or a Star TL.
If I were only able to throw one company's molds under the sponsorship, it would still be Innova, but I would have to go back to trying to beat in Destroyers or bagging some combination of Destroyers/Terns/Bosses instead of just Scorpiuses. I like the Scorpius an awful lot, but I think the combination of Colt/Pig/Roc/TeeBird would still outweigh it.
Honestly, my second answer would probably be Prodigy, not because I like the company, but because I bought most of their molds when they first came out, and I definitely think I could build a very sold bag with just Prodigy molds. I haven't thrown enough Trilogy molds to be confident with them, and their molds I have thrown never really clicked with me.