The biggest problem with Dom III

[Archonsod]

Xietor said:
for the advanced player, you may want to play a MA race, and add some EA or LA empires to create more of a challenge. It would be an option, not a requirement.

There's plenty of ways to give yourself a challenge without actually needing to alter the Era system. Try imposing some rules on your own pretender build or similar (no bless, no SC and the like). I'd argue that this would be way more effective, since the challenge of another era nation depends heavily on other factors (for example, EA national troops tend to have lighter equipment, and would likely struggle to expand in a late era game).
The same applies to multiplayer games. Turn the site occurence to minimum and let your opponent pick a nation less dependent on magic (like Ulm) while you take one heavily dependent on it (Caelum).