The problem is, more episodic shows are generally more lucrative. B5 struggled throughout its run to stay on the air, and its successor, Crusade, despite being more episodic in nature, died quickly. B5 never attained the same name recognition as Star Trek, and never will, in part due to the fact that Trek is/was more episodic, and theerfore easier for the average viewer to get into. The general public often needs time to discover a show, and if, in the second or third season, people start to check it out, a continuing storyline will likely drive them away; viewers will feel like they need to "catch up," and few will be willing to try and do so. Star Trek benefited from its episodic run, and that's why it's much more mainstream success-wise.
I loved B5, and I like Andromeda quite a bit. I like story arcs. But, the truth of the matter is, I am not exactly the type of person a show needs to attract. What I like is not what the vast majority of TV viewers like. If shows like Andromeda need to ensure their futures by compromising a bit, then they should do it, by all means. I'd rather the show survive than go under because it tried to cater to a specific, small demographic which has never proven itself to be major consumers to advertisers. Even Star Trek, while successful in scifi terms, is still not that powerful a name brand - that's why Enterprise is on UPN and not one of the "Big 3" networks (which, despite serious erosion due to cable, are still the major players) and all the previous series, except the original, were syndicated. Even the original never really made it big until it was syndicated. Even then, "big" is a relative concept, since even the most successful syndicated Trek series would have been quickly cancelled by a network, because its ratings aren't really competitive with network shows.
Advertising fuels the TV industry. Without large numbers of viewers, and the right demographic breakdown, advertisers don't bother spending their money. Without that revenue, there is no show. So making Andromeda more episodic may be better for it in the long run. I am a bit leery of the show losing a major part of its creative team, though.
But the new Trance is pretty hot. I still find Lisa Ryder (Beka) more attractive, though.