There will be new prototypes but you still will only be able to have a maximum of 3 out at a time. Will the new protos change strategy, yes. Will they make it more difficult to raid, only time will tell.
I think where we will gain back offense is on the new tribal boosts. This is good news for endgame players. It?s probably going to be bad for players who have reached the point that they regularly face bases with protos but don?t have the tribal boosts yet.