I actually couldn't disagree more with many of the sentiments here. I think there are two complaints many players are having here, so I'll try to give my support to them individually.
1) Elimination Rounds:
I am a huge fan of elimination rounds! I believe the height of any competitive event should be an elimination round. This is as true in Sport as it is in Netrunner. The champion should always win their final game in my mind. There should always be the pressure of "win or go home" at some point in the tournament. Every player should know "if I win this last game, I'm the Champion."
Swiss play just doesn't give that pressure, since the final result will often be dependent on more than one game. Worse yet, if we have complaints about the imperfection of tiebreakers NOW, imagine if it decided the winner of an entire tournament!? Even worse, it would realistically remove a huge percentage of the players from championship contention halfway or three quarters through Swiss. There is something to be said for scraping through Swiss to sneak into Top Cut and then rampaging through the Elimination rounds to win the whole thing. It's fun. It's dramatic. It's exciting to be a part of and exciting to watch.
Finally, and this will probably be a point of contention to many of you, the best player will not always win. This is a huge boon for me and the entire point of a tournament in the first place. We all play against players who will beat us 8 times out of 10 or decks that beat us 8 times out of 10. So why play a tournament and not just do a big league, clearly identifying the player who has the best win percentage? If you find this as displeasing a thought as I do, you should be a fan of Elimination Rounds, at least in large tournaments. Elimination rounds throw out the percentages. It doesn't matter if you're in your worst match-up or playing your greatest rival. You just need to win 1 game. Variance will ALWAYS be a part of more than just your decks. It's a part of any competition and should be embraced.
There is no doubt that double elimination is brutal. Until I hear (or think of) a better option, I will support it though. In response to intangible stakes and transparency, these are mainly an issue of unfamiliarity with the structure. I've now played in two Regional Double Elimination brackets and clearly understood in every game what I was playing for. If I win my first game, I'm in the top 6, great. If I win the second I'm in top 4 and get an Andy, amazing! Agreed, it gets slightly convoluted once you hit the Loser's Bracket. Still not to the point where a player intelligent enough to play this game at a high level cannot figure out.
As to irregularities on the sides you play, there is no doubt that playing losing on two consecutive Corp/Runner games is painful. That being said, at most 1/4 of Top Cut can face that problem. In addition, it promotes parity in your Runner/Corp strength (as does WSW). I'll concede that it's not ideal, but it's an acceptable negative of the format.
Playing an opponent three times in Double Elimination is ONLY possible if you are both in the Championship game and it goes to a final "winner takes all game." I don't see a problem with two of the clearly top competitors of the day squaring off an extra time. In fact it also necessitates that the players split the first two games in Elimination play. A third game, creating an effective Best-of-3 sounds ideal rather than a negative.
The depth of the match-up is multiple issues. Firstly, if you lose your first game it will take MORE wins to reach the Final. You may like or dislike that, but it as an inherent part of Double Elimination. It actually puts higher stakes on the early games of DE, which I quite like. Winning early and often is clearly an advantage, and I think rightfully so.
The second issue about waiting is a problem, I'll agree. I've also been on both sides of the Championship match, once having won the Winner's Bracket and once having won the Loser's Bracket. It's tough for different reasons on each side. Once again, until presented with a better option, it's acceptable.
I am a huge fan of the current system. I think Weak Side Wins as primary tie-breakers are a good choice (promotes parity). I think Elimination rounds are absolutely necessary at large high level tournaments. They are simply more dramatic and decisive. I also find them much more fun. Double Elimination, despite it's flaws, is the best solution I've played/heard of for Netrunner. It's a brutal format, but it's rewarding to those who slog it out. Winning the Finals from the Loser's Bracket SHOULD be more difficult than from the Winner's Bracket. It's not impossible (already happened at a Regionals iirc), just properly difficult.