The alternate scenarios are based on the Empires in Harm mod, which updates the original game. There are light ships, transports, and piracy rules for the naval action. Most countries have Order of Battle changes to the corps, strength factors, and morale. There are also some diplomacy adjustments to the national modifiers and influence numbers.
I think most players (still playing) are interested in the updated alternate scenarios. Many grognards who played the original EIA boardgame seem to be adamantly opposed to the EIH version and complained over the years about how this PC game was not faithful to the original. Which is why I spent so much time implementing two separate versions, original and alternate. The hope was to attract many of those grognards back to the game but that hasn't happened. Maybe with the upcoming v1.23.08 official update and its many bug fixes we'll see some renewed interest. Maybe, we'll see.
Anyways, short answer to your original question is to probably play the alternate version. If you ever get into a pbem game, it will be easier to go from alternate to original than vice versa. Hope this helps. Enjoy!
Empires in Arms Development Team