When merging the two, you definitely have to consider the technology. As others have pointed out, Federation technology is more on par with Centauri and especially Minbari levels than Earth or Narn.
With the exception of cloaks (which, by the 24th Century was more due to politics than technology levels) and the Romulan's quantum-singularity powered Warbirds, most of the major races are on-par, technology-wise. You'd have to come up with an interesting backstory why that's the case and yet, the Narn are so far behind. The Centauri occupation could explain this, to some extent.
The other major issue is the technology in Star Trek
is a bit more, um, shall we say, theoretical, while JMS consulted with NASA's Jet Propulsion Labs for Babylon 5
. Thus, Warp vs. Jump Gates and the existence of transporters would also be tricky issues. Setting it in the time period of Enterprise
, when the transporter was still relatively new might help with that, though Babylon 5
, itself takes place, for the most part, from 2257 ("The Gathering") to 2262. "Where No Man Has Gone Before" takes place in 2265.
I think you could work it if it was in an alternate reality which is a mix of ST
. In 2265, the Interstellar Alliance is in its infancy and could easily be merged with the United Federation of Planets. After forming the IA/UFP, in a universe where the Vulcans were as equally involved in the Babylon Project
as the other races we saw in the show, they could have to deal with the Klingons, who see the IA/UFP as a threat. Of course, the first reported viewing of a Romulan could still occur in 2266, with random sightings and rumors being mentioned previously in this "new" amalgamated universe.
As you can see, as a kid, when B5
was still on I thought about this and continue to do so on and off as a mental exercise. It does bring up some interesting issues to figure out on a sleepless night or when I'm bored!