If I were to pick a team with Thor on it to go up against another team that had a FTL speedster, I wouldn't choose Thor to go up against him. Assuming that I had an FTL speedster on Team Thor, he'd be my go to. Thor would be placed against the opposing teams power/tank/blaster. Playing on his strengths would be the wisest choice, because unless Thor has some way of drastically slowing down time, the FTL speedster would logically pick him apart. It is what it is.