Actually yes, there was a second run.
Counting all of the ones we know were in FS2 (all of which could be potentially destroyed), Warzone, and Derelict there would be about two Aeoluses left.
Several FS2 Aeoluses (and other ships) as well as ones from Warzone and Derelict are in the campaign.
However, there was a demand for the ship so a new variant was constructed in the five or so years since Warzone. (older surviving ships have also been refitted)
Slightly more powerful beams, longer range flak, etc.
There have been a few GTVA experiments in cruisers using meson cannons... nothing came out of them.
Also I don't see what's so unrealistic about a second run of the Aeolus. There's a precedent for it in FS, the Leviathan being a modified Fenris hull for the V-T war.
As opposed to declaring a second ship class though, these are just rearmed Aeoluses.