well, i know that jerry was very good at picking scales and playing with the rest of the band, but i read an interview of him and he says that he often plays in different time as the rest of the band, theoretically, you could do this with scales too. what you can do is find a scale that is in a different key as both of them but compliments them at the same time. in that case you can stick to that scale the entire song. so say the changes are A - E you can find a melodic scale in B and stick to that. this works if you can find the perfect scale but often sounds cluttered if you pick a scale or key that doesnt work well together. so this is only used sometimes but can work well.
this was actually something that ive heard of recently and only tried it a couple of times so let me know how it works for you guys.