I'm going to buy a traxxas Summit soon and i was thinking of switching to A123cells becuz of their faster recharge times. now a 2 2s packs only gives me 13.2v but a 5s pack will give me 16.5v. i want to get close enough to the maximum of 16.8v

so here is my question, if i put a 3s pack on one side and a 2s pack on the other would the esc react differently to if i put a 5s on one side and nothing on the other?

It is the same end result for the motor/vehicle , but the bec may be overloaded using 5S on it. A 3S and a 2S would be better choice.