Suggestion for the senate and/or other Roman factions if you don't want them in the way:
Just give them one-unit armies at the beginning of the game with no cities, and they will immediatly die off at the beginning of the first turn, thus fulfilling the need to have them in the game, while removing all the hardcoded mechanics that come with them. You will get "Faction Destroyed" messages every time, but that's no big deal. Even though you lose 4 factions, you're still left with 16 to work with, which should be lots for a map this size.
The other thing to consider is the victory condition of conquering Rome. I would suggest you make Rome the Macedonian capital, that way they don't have to worry about it, while the other factions must take it in order to stave off the conquering Macedonians. Or make it the Persian capital, to insure AI Macedonians will concentrate on conquering the Persians (in theory), and making playing as the Macedonians a little more historical.
Cheers,
Bacchon
-edit-
Oh, and another thing. If you end up using the Roman factions (perhaps as the Phoenicians as Accouting Troll seems to suggest), you can avoid the Marius Reforms event by disallowing the Imperial Palace, which it's tied to. To maintain the same tech-tree, just create a new building that is exactly identical to the Imperial Palace, except called something else.
-further edit-
Gah, check my post here.
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