If it's a merger of histories as well as technologies, I think replacing the Dilgar War with the Romulan War would make sense, but instead of leading to the Federation it would just solidify Earth's status as an interstellar power, as the Dilgar War did in B5. That would keep the Shadow War as the impetus for the Federation. In this amalgamated universe, the Vulcans would probably be the Minbari, the Andorians could be the Centauri, and the Tellarites could be the Narn. The Romulans could also take the place of the Drakh.
Maybe the NX-01 of this universe would use the fusion power sources and laser- and missile-based weaponry of B5's Earth Alliance, and then post-Shadow War Federation ships would have more advanced technologies thanks to the Minbari and Centauri.
's last point, as a fan of fighters (both real and fictional), I vote for keeping the Starfuries.