Okay, here's the big one: create four new techs: Law, Chaos, Good, Evil. Give each civ two of those techs, a la D&D. Certain units can only built by certain alignments. This would mean that you'd have to take out the Great Library, but I think it's worth it.
New tech: Necromancy, requires new resource: graveyard, and the Evil alignment. Allows you to build skeleton versions of existing units that cost half as much to build, and cost no maintenance, but are only half as powerful as well.
Deities: have various types of temples that can be built in cities that offer different bonuses. Base the types of temples you can build on your alignment, so for instance only Good civs can build temples to the fertility goddess, and only Evil civs can build temples to the god of death. You could even give each temple the "this replaces all other buildings" flag, so that each city can only have one temple in it.
Add five new resources - Air, Earth, Fire, Water, Nature. The resources you control determine what spells you can cast.
Make civs for the various races, e.g. elves and dwarves. I find it easier to get into a game where I'm familiar with the civs than when I'm not, and everybody knows who elves and dwarves are. Nobody knows who for instance the Ostian Empire is. Also, make your existing civs more archetypical - make a Lawful Good paladin-type civ, a Chaotic Evil civ that leans toward magic use, a nature-oriented civ with free access to the Elves and Nature tech, etc. If each civ has a distinct personality, I'm more likely to care more about who I play.
That's about all off the top of my head. I'm sure I'll think of more later.