Orders of importance IMO:
Speakers > HU > Amps > Processors > Wires
I feel a good sources is very important and each sounds very different from another. Going from a 100 HU to a 1k head unit one could easily tell which is better. But when you reach the high end head units, whether one is better than the other or not, that is a matter of preference. For example, a Mcintosh mx5000 and a alpine f1 7990, both sounds greatttt, but at the same time it sounds so different its not even funny. The mac was rich and warm with better dynamics and control in the midbass/bass region, while the f1 has more top end and a breathiness to the vocals and the sax that was also awesome. Team Mac would say the Mac is the best HU in the world, team F1 would say theF1 is the best in the world. It was hard for me to even decide which I liked better.
So back to the OP, will changing the HU alter the sound of your entire system? Definately!! So find a head unit that suits your taste, they all sound very different.
hope that helps!