I'm not really a connoisseur when it comes to SoaSE, but I do have a suggestion... you could rework the tech trees (if that's moddable) in such a way that pursuing new designs is always an option, but never a necessity, in order to not fall behind in technology.
What I mean is that you could have a single shipset for the game (which would probably reduce the workload and balancing/playtesting time to a significant degree) made up of the most emblematic ships from each of the different eras, and just leave it up to players whether they want to research the new prototypes or improvements to the starting ships instead.
Someone who prefers the WC1/2 era could just focus research on improving current designs (stronger armor/weapons/new abilities/etc), while others could favor researching the new prototypes (WC3/4/Prophecy ships).
Since the game is real time, nobody would have a real advantage: the guy investing his time in new ships would not have done many upgrades for them, and the guy investing his time in upgrades would have made his old ships become as good as the non-upgraded versions of newer ones.
This could also make multiplayer more interesting since the battles would not always feature the same ships, but would instead depend on each player's style. In one game you could have heavily upgraded Ralaris attacking the Behemoth, while in another game you could have Hornets successfully holding off a Hakaga attack (Landreich anyone?).
I do know that SoaSE has all sorts of crazy tech trees (technologies that are required in order to train others, technologies that affect existing designs, technologies that allow for new designs, etc), so you could probably integrate all of this in a way that is true to the WC continuity.
For example, everyone could start without Phase Shields, as in the WC1 era, and Phase Shields would be a researchable upgrade that would strengthen the shielding of all existing capital ships - then the other player would need to consider researching Torpedoes, which would increase the damage done by bombers to shields, in order to keep up with Capital Ship technology advances, etc.
Short version: I think this is a much more interesting approach than selecting different shipsets from the game's launcher, it avoids splitting the game into different games for different fan groups, and saves you the trouble of having to make each era feel unique (while still keeping them balanced!) rather than a retexture of the other eras.
Damn, now I want to make a WC RTS mod too.