In my opinion upgrading a alternator doesn't make sense, except you have a huge NEW battery bank or a lithium bank.
The cause of poor charging systems with insufficient performance is usually old, worn-out lead-acid batteries.
As tiger79 mentioned, you will never see current of 100A with such batteries.
If you're planning to upgrade your alternator, you have to care not only for the cross section of your cables, but also for your diode-splitter as well.
I would also recommend bigger crosssections for the cable. Keep in mind, that the electric losses rely not only on current, but on voltage too. The generated power of your alternator is power= voltage x current. If you have a voltage drop of 5%, you have a power drop of 5% too.