For me, I think it might just be psychological, BUT... someone I feel that before the server refreshes at 5am every morning, so basically before I head to bed, I leave my team of 4 as the main with my 3 lowest power ninjas, or even just have my team become just my main and leave the other slots all empty. I somehow feel that my match up for survival is easier.
BUT I REPEAT... I think its just psychological. I don't think it actually makes a difference.