Damn, damn, damn! I write a long reply, and CFC dies on me! Ok, here we go again ...
Galgacus: If I understand you right, you think a Peloponnesian War scen ought to be a "pure war" scen? If so, I must disagree; political scheming, backstabbing and defection played a big role, and the only way to represent that is to have a mass of civs in a mess of alliances.
As Xen said, read the whole thread, and you'll find plenty of ideas on how to make major cities hard to take, make overseas communications critical for Athens, handle the Persian factor and many other things.
The idea for a "Persian Alliance" wonder for Sparta is good, and I even know how to improve it; make it require a resource only found in Persia, so that the Spartans can't build it if the end up in war with the Empire. It could be a luxury, called say "Eastern Goods", and Persia would have enough it could trade to any friendly civ, so that the Perso-Spartan alliance will not be prevented by Syracuse buying all of the resource or something equally stupid.
As regards the map, I'd like one including less of the Balkans and Italy, but we don't seem to have one available. The idea of leaving big parts of the map empty leaves me cold, not only because it would practically force us to disable setttling (which we'll regret the moment the AI starts razing cities), but also because it gives a false impression of the intra-Greek conflicts taking place in a vacuum. So, I do believe filling out the extra space with artificially weakened civs is the best solution, especially as it increases the opportunities for diplomacy and trade.