I found no evidence of Kane naming any bases ever

But maybe I missed something.
It's a thematic remark. Kane is very much a charismatic self centered egomaniac with a messiah complex. He is not the sort of person that would name cities for his generals. Can you imagine Stalin naming cities after his generals?
As for the rest my reply is simple. Real city names weren't trying to fit a theme. They just randomly happened. We are. And honestly I think we are both failing.
Everything we did so far, but especially that last list you made just feels... off to me. I just find them to be cheesy and really forced. Especially those few named after characters. Those really just felt like too much. The rest... I think we can work with, sort of. Basically hear me out here and you'll see what I mean.
Long story short I did a lot of thinking. And I think I know why we are going wrong and what we should do to rectify that.
Put simply I really think that the direction we should be heading in with this is trying to get into Nod's head, so to speak. How would the Brotherhood of Nod name cities if it founded them? And honestly I think that to do that we might be better served drawing from the Nod mythology and theme rather than existing base names or people.
Basically think of SMAC city names. I assume you have played Alpha Centaury.
If not, stop everything and play that game. It's the only one in the Civ series better than CIV4. Anyway, Nod as a faction has a lot more in common to SMAC factions than it does to any culture, religion or state from our history. And so I think we might do best to try and mimic that sort of naming style.
And in that game each faction had a bunch of names all influenced by their ideology and core theme rather than any significant person or place.
Like the Hive didn't call it's cities "Yangtown". Instead they had "Worker's Nest" and "Discipline Tubes", stuff that invoke the image of a human hive. Equally the Gaians called their cities things that invoke an ecological utopia such as "Gaia's High Garden" and "Children of Earth".
I think that really we should try and and look at Nod holistically and try to come up with names in that style that fit the prophecy and mythology of Nod. Basically look at their slogans and ideology and try to come up with something that evokes that.
Now that is admittedly easier said than done. And we will probably have to fill the ranks out with names from our previous lists. But I really think this should be the focus for at least the first several cities.
It would be really nice if others would also join our little brainstorming and give some input on it. This one vs one is not leading us far right now
YES, yes it would.
PS. A small note. If you are naming cities after characters from a Slavic ethnic background such as Slavic or Oxana you should probably not go for the Germanic -burg but the Slavic -grad suffix. That's the standard one used in Slavic languages for this role. Example: Stalin
grad, Lenin
grad, Petrov
grad etc.