Ultimately, all the power for your car audio system needs to come from your alternator. If your alternator simply isn't up to the job, then no amount of extra capacitors or extra batteries are going to solve the problem.
I don't have a problem with the use of power supply capacitors, for the purpose which they were designed. I don't agree that they put a significant additional load on the alternator; they're very efficient devices. But if your alternator is consistently overloaded, then a capacitor won't help. Capacitors shouldn't be marketed or sold as a way to take the strain off an undersized charging system.
Upgrading the "Big 3" wiring may help a bit. The Big 3 consists of three primary wires in the charging system: the wire between the alternator's positive output and the positive battery terminal, the wire between the negative battery terminal and the vehicle chassis, and the wire between the engine block and the chassis (as this is the alternator's ground connection in most vehicles). Your stock wires are probably undersized, and you may be losing some voltage because of this. But while upgrading the wires may reduce the amount of voltage drop on this part of the system, it won't make your alternator produce more current.
You have two choices: increase the current supply, or decrease the current demand. Increasing the current supply means an alternator upgrade, because the alternator is the ultimate source of all current. Decreasing the current demand means making your audio system more efficient, so that you can get the same output level with less power draw from the charging system.
If your subs are currently in a sealed box, you might look into having a ported box designed and built for them. This helps with deep bass extension, so that some lower frequency sounds will be louder, without using more amplifier power. A ported box will have to be larger than a sealed box, though; and it would probably have to be custom made for the square L5 subwoofer.