Babylon 5, without question.
Trek assumes that we do away with too many things that have made humanity what it is. Yes, it's 200 years in the future, but just look how little progress has been made from the 1800s until now. Prejudice always has existed in human society and will quite likely continue to exist for a long time to come. You know that large groups of people, religious or not, are going to react poorly to first contact with another race, even if that occurs in another 150 years. Really, the most outlandish part of Trek is that everyone is all communist. Considering the vehemence that Socialism engenders in people now, and how widespread capitalism is, I find it extremely difficult to believe that only the socialists will survive the mass destruction of the human race.
That's another sticking point for me. B5 is predicated on the idea of a multitude of nation states, none of them really super powers. Trek is based on the old cold war idea, with the downfall of mankind the result of those two powers going to war. B5 takes the approach of warring states, terrorism, and totalitarian governments to pull humanity downwards and caused the dissolution of the UN in another 100 years. Now, while the Federation is obviously communist, Earth Alliance is a very military organization. Frankly, from history, this seems the more likely method for governing a large number of people. There are also shades of imperialism present, in the way the EA treats its inner and outer colonies, much like how the great empires of the past did here on Earth.
The technologies represented in Babylon 5 are also more kosher. For one, their power system does not explode when a far off section gets hit, indicating that they've retained the technologies of the fuse and the circuit breaker. Oh, and the jail cells have actual doors, making a jail break a little bit more involved than just cutting power.
Another thing with the ships is that there are actually different classes of them, with distinct purposes! There are corvettes, battleships, and destroyers, each roughly corresponding to their 20th century naval counter parts, in addition to cargo freighters, passenger liners, and long-range exploration vessels.. These are designed to act as anything from escorts to planetary invasion platforms. In addition to the fact that fighters are used for defense of these capital ships, they also have active defense grids that will destroy incoming enemy projectiles before impact. When was the last time on Trek anyone got the bright idea of trying to shoot an incoming torpedo? Oh, and these ships use actual battle tactics(!) something I don't think we'd forget in 250 years.
That's something else about trek; they're not students of history and they have very little imagination. Anyone with the know how care to calculate the energy with which a ship the mass of your average Federation ship going at even low warp velocity will unleash if it impacts a planet? You'd think that someone would have figured out what a marvelous terror weapon that would make. You'd also think that someone would realize how nice it is that space has three dimensions and that ships don't have to sit on the same plane shooting at each other.
Another thing that I disagree with is Trek's Prime Directive. Sure, that might work on the military, but there's no way that you could keep the merchants out of an area they could exploit.
Oh, and with all the talk of US annihilating ourselves, why has no one brought that up in relation to Trek? On B5 there is good evidence of lots of races of all tech levels dying off for one reason or the other and leaving their worlds behind. That's almost never seen on Trek. Also, the people on Trek never seen that interested in all the powerful tech that crosses their paths. At least B5 has companies like IPX which make it their business to gain an advantage any way they can.
In the end, I think B5 wins because there's nothing really unrecognizable in it. The social structures that the Earth Alliance is based on have shown themselves in the past to be amongst the most stable and long lasting. The ones that Trek seems based on have either not lasted even a century or were never truly implemented in the first place.
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Reference 1. Reference 2)
-- Jack
On B5, understanding is a three-edged sword. On Voyager, it's a dull butter knife.
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http://www.infoshop.org/sf/voyager.html