Sorry for the late reply, but I have been stuck studying for those damn finals
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I'll try and get a post or two in everyday, until 2 weeks from now that is, there will be multiple annoying posts, by myself, everyday.
Noldodan, as I have said, (and I think what mrtn\Celeborn agreed on) the best way I think we should go for ages would be:
First Age
(middle-late first age, with the arrival of man)
Time of the Rings
(Elven supremacy and Saurons Power)
Time of the Númenóreans
(Supremacy of Man, Numenor and it's later subdivisions\War of wrath)
Third Age
Best known, time of the peace, yet weakened state, time of the fellowship
All who agree say nay,
I mean ye. 
I know many of you *cough*Celeborn*cough* want to have a setting of Twilight and much older starts. So, once the actual MOD is out, it wouldnt be to hard to devote a update to such a starting and throw in some wonders\units\updated techs. Remember, we want to please all Tolkien fans, or at least as many as possible. Celeborn represents on of many, I am sure
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Civilizations.
Well I cant argue with embryodead on his excellent point. But mrtns point about having better, more complex civilization, even if that means fewer, is compelling also.
So, Ill just name one at a time, one we all agree on for now, wether the later project has them is up to a vote, Im sure
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Gondor.
King: Thats a hard one. I personally would go with Isildur
UU: City Guard? Another hard one, what I am thinking of can be found in the Return of the king, page 25, second paragraph.
I was also thinking we should use some Roman\Greek type units for them, in the third age. Just for flavor, unless of course we give them and extra hp or defense or something.
Bonuses: Militaristic and Commercial perhaps?
Cant say what Techs they start with, as we dont have them.
Color: White, IMHO
Flags-
Governor: Manage Production and Citizens
Build often:
Defensive land units
Trade
Growth
Production
Title: King if its Isildur\Strider, Steward if a steward...
Aggression Level: Id say medium for regular game, more if its fixed alliances and locked teams.
Gender: Male
Cities(at least the ones I can think of):
Capital: Minas Tirith (or Osgiliath?)
Minas Tirith
Pelargir
Osgiliath
Dol Amroth
Cair Andros
Lossarnach
Pinnath Gelin
Ringló Vale
Calembel
Linhir
Blackroot Vale
Ethir
Tolfalas
Anfalas
Lamedon
Langstrand
Ethring?
Harlond?
Great Leaders:
Well, Ill leave this part up to some one else, it should be easier than the cities anyway
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BtW, I got a lot of info from
The Encyclopedia of Arda and most of the cities from Return of the King.
AlcTrv- For some reason I am thinking 007, but besides that, a good idea. I wish we could upgrade them three times, actually. for the first 2 eras they are immobile, and for the third, they are on black horses, and the last on the beasts, as you say. But I don't think it's possible, and it is somewhat inaccurate for the First and Second eras. In fact, even in the second to last era. Only in the Third age were they powerful. They aren't really a UU, more of a bonus.
Perhaps a good UU for Mordor would be the Wight? They wouldnt have to be restricted in number.
A one-city Numenor stuck on the island, and Gondor filled with orcs and Dunlendings would not be cool.
but don't sacrifice too much races...
But at least I can rest easy with know one but you catching it. The war of wrath was the title of the Great battle when the Vanyar came to middle earth (then left)? Is there something I could have confused this with at the end of the second era? The Last alliance? Changing it to Minas Anor would be a good idea, but I disagree about Minas Ithil, as we are already short on cities for Mordor. And putting the same city in with two different names is a bad idea IMHO. A similar example would be: Should we include Orthanc in the list? No because we need it for Isengard. 
