Honestly I'd prefer to lump HRE and Byzantium with Rome using the new leader system. Since different leaders almost represent different civ I-III civilizations and those "civs" have very close ties.
On the other hand I'd also rather see the cherokee, Iroquois, and Pueblo as seperate civilizations because they really don't have any common ties in language, culture, or location.
Unfortunately there will always be people on the forums who feel strongly one way or the other, and we could argue forever. One thing is certain . . . after the developers have put all the work into making a whole seperate civilization it's probably too late to ask them to change things.
They aren't going to combine three civilizations/leaders into one, even if it will sound odd to have the romans warring with the holy romans, or even the byzantines. Nor do I think they will MAKE three other civilizations that I feel should be included to replace the two I think shouldn't exist at the same time on the same map.
It's a done deal. The work has been done. I'm sure someone was consulted over the decision, I hear rumours of polls. I missed those so my vote, all our votes, won't count till the next expansion, or until the next version of civilization.
The native americans are in, the pueblo, iroquois, and cherokee are not, the romans, byzantines, and HRE are in, I doubt I'll see a new spanish leader, or to make my point very clear Hitler.
We could argue forever. But why? Does it really alter our game THAT much?