So basically it would have scenarios like this:
Mandalorian Wars=Republic vs Mandalorians only
Jedi Civil War=Republic vs Sith Empire only
Great Galactic War=Republic vs Sith Empire only

And as basically everything from armor to ships to ground vehicles changed a lot between Jedi Civil War and Great Galactic War, choosing one of these three scenarios would limit you to just the things that were used in that era.
For example, if you play Republic in Mandalorian Wars and Jedi Civil War, your ships would consist of things like the Foray-class and Hammerhead-class while ships like the Thranta-class and Valor-class are not available at all.
Similarly, when playing as Republic in the Great Galactic War, you would not have Foray-class and Hammerhead-class ships and instead Thranta-class and Valor-class ships are your standard ships.
The Sith would similarly have access to the Interdictor-class only in the Jedi Civil War and Harrower-class only in the Great Galactic War.

Heroes would work the same way, in the Jedi Civil War, Republic would have Bastila Shan as a hero unit and Satele Shan in the Great Galactic War. Similarly, the Sith would have Darth Malak as a hero unit in the Jedi Civil War while in the Great Galactic War, they would have Darth Malgus filling the same role.

Armor would also need change of course, as during the Mandalorian Wars and Jedi Civil War, the Republic wore those red, black and yellow suits but by Great Galactic War, they had clearly taken inspiration from the Mandalorians and started wearing proper Star Wars armor. While the Sith wore different armor in the two conflicts as well, as they were not the same empire and instead just two different empires following the same ideology.

Another interesting idea for a scenario would be Jedi Civil War Sith (Revans Sith Empire) against the Great Galactic War Sith (True Sith Empire), considering that Revans intention in taking over the Republic was to prepare for the True Sith Empires inevitable invasion.

Then there could of course also be these mixed-conflict scenarios like the game currently has.

The mod is still definitely a work in progress but it shows promise.