No, it's not nessesary, but it will save you alot of headache in the future. Especially if one of the batteries is older. It won't charge to as high a voltage, so everytime you turn off the car, the main battery will drain the second battery. In some cases, the two batteries will then take turns draining each other all night, till you wake up to two dead batteries.
An isolator also alllows you to run the system with the engine off and still leave you with a fully charged battery to start the car, because your only running the sound system off the second battery.
2 gauge is good for 200 amps. How big is your alternator? There really is no point in using fuses larger than your alt can power, so it would be safer to fuse the system to your alts maximum output. Assuming it's less than what the new wire is rated for >200 amps.