+1 on WestTN's reply. In a multi-battery setup, if one battery goes bad both should be replaced. The older battery will have a different internal resistance than the newer battery, which will result in a lower voltage for a given load. So like he said above, the stronger battery is not only carrying most of the starter load, but it is also trying to put some juice back into the lower-voltage battery at the same time. That'll accelerate wear on the new battery.
Then when the batteries charge after the start and during the normal truck-running state, the stronger battery will boil as the system continues to try to bring up the weaker battery. Same effect as leaving a battery on a trickle charger (not a maintainer). Again, more wear on the "good" battery.
An isolator works great for things like winching or other high draw applications, because you'll always have a backup battery available. Like Road Dog says, if your batteries are dead after a couple of days there is something else wrong with your truck. They don't "swap current back and forth" as they sit; the batteries will reach an equal voltage (again, why two same-aged batteries are needed) and then stabilize. Mine sat for about two months at one point and the truck started just fine.
Save your money on the isolator and fix the problem.