If you play with people who apparently care about things like being "fair" (like I do), 2001 wins, hands down.
You'd have to ask Mike, or even the legendary Eric & Todd what the original mood of the game was, but my impression from the 1998 and 2000 rules was that it was designed to be humorous, laid back, with an attitude of "as long as there's big explosions, we don't care who wins".
Unfortunately for NELUG, we sort of got into a tradition from the get-go of having serious gamers involved who wanted to do things like "win". These sorts of people take one look at a spearman rolling an automatic success (a 6, let's say) with a required UR of 12, and say "Oh, come on! He can't hit my F-16 with a freaking spear!" Then, when the rules dictated that the pilot would need to make an emergency pit-stop, they'd throw some sort of hissy fit about how stupid that was and how there's no way a spear thrown at a fighter jet could possibly result in such ridiculousness.
So NELUG quickly resolved to handle such situations by attempting to be "fair" and follow "reality" whenever the rules were unclear, arbitrary, or otherwise subject to interpretation. This had the end result of less silly combat, but calmer players who weren't royally pissed off.
That's where the 2001 ruleset proves to be the most superior of all the rulebooks. It's the most complete and most realistic in terms of possible options, and the least silly. It meant that Shaun and I could point at a specific passage in the rulebook whenever someone would blurt out such objections as "He can't do that! That would never happen!"
The downside to the 2001 ruleset is that it's so crazily complicated that you have to attend an 8-week course in order to really understand it (Tuesday and Thursday nights, I believe-- I did the one offered by Franklin Pierce since it was cheapest). Anyway, getting new players is very difficult, unless you get them to play with you a few times first, THEN have them read the rulebook. Otherwise, people are so intimidated by the tome that they'll just opt out.
The 2005 rulebook, by contrast, is far simpler. So people can read it more easily and it's more inviting with its HTML version and all.
Anyway, my honest opinion is pretty biased, since I've been playing with the 2001 rules since around 2002 or so, and I have yet to actually PLAY a game (with other humans) with the 2005 rules. So I've got a fair amount of the 2001 rulebook in my head. And if I ever DID play with the 2005 rules, I bet I'd suddenly be making mistakes like using the 2001 rules wherever the 2005 rules didn't specify exactly what happened.