Ok, here's my city list; I can expand on it any time you'd like. I tried to keep out cities founded by Arabs, and find it abominable that they invaded Nubia (although I don't dislike Arabs at all, and realize it was only a small group of people who perpetrated that horrific act, Arabs in general are cool), but sometimes it's hard to distinguish the names. Use any of these that you'd like, but please take out the Arab cities from the Nubian city-list, no offense intended at all but it tends to detract from the "flavor" of the civ. More cities to come soon.
Capital:
Kerma (first capital, founded 5000 BC, oldest city in Africa)
Napata (capital during Egyptian occupation, sacked in 591 BC by the Egyptians and Greeks)
Meroe (After 591 BC, capital moved to Meroe, since it was an island and more defensible; well known and important)
I'd suggest Meroe, since it is well known as was important, but it's your mod, so choose whichever you'd like.
Other cities:
Kerma
Meroe
Napata
(Whichever you didn't choose as capital)
--------------------------------------------
Here, I'd like to suggest placing one city for each different small state that was absorbed into Nubia. Some are Nubian names, and some are Egyptian names for Nubian tribes or nations; no one is really sure how to tell on some of them, so I'll list them all together.
Irtjet
Wawat
Zatju
Medja
Kaau
Sha'at
Iryshek
Tua
Imana'a
Ruket
Awshek
Webetsepat
Tjemehu (these I'm unsure about, they could have been Nubians, Libyans, or the result of a mixing of the two peoples.. they could've been part of C group)
Kush-Yam (or sometimes, simply Yam; you make the call)
Nubadae (one of the Christian Nubian peoples)
--------------------------------------------
And now, for some simple Nubian cities
Dongola
Aniba
Toshka (also called Mi'am)
Buhen
Semna
Ballana
Mirgissa
Korosko
Premnis
Dakka
Hieraskaminos (dunno about this one)
Makuria (a small Christian Nubian state)
Nobatia (the small Christian state inhabited by the Nubadae, I think.. might be best to choose just one)
Alodia (yet another small Christian state)
If you need any more info, I'd be glad to help. This is my absolute favorite region ever, it's incredibly interesting.
Oh, I forgot to mention.. in the hills of eastern Sudan and Ethiopia, there're a group of people known as the Nuba hill tribes; they're descended, I believe, from a group of Nubians that fled Nubia after an Egyptian invasion. They re-settled in the hills to the East, and have an interesting and unique culture. Perhaps you should include some of their cities, as well, if I can find any?