To me, it gives you expandibility and MUCH more control over your stereo and you can run an active setup using a processor.
With a processor you have the ability to control the frequencies through which your speakers play; rather than having a passive crossover tell you. And you can always change these settings anytime you want; no more being stuck with what the manufacturer thinks works best even though they've never sat in your car nor know your preferences like you.
From there you can also dial in the way the music sounds via EQ's. Most h/u's come with EQ capabilities but nowhere near as refined as most off-board processors.
Then, finally, you have the ability to control time alignment which is already discussed above.