Edit: Some great comments here. Thanks to everyone who made meaningful contributions to the discussion!
I have three arguments for why the tournament point system is just plain bad.
The first issue is that losing has different penalties for how bad you lose. If you only just lose you can still score 5 tournament points, if you lose badly you only score 1 tournament point. The problem with having a bigger penalty for a bigger loss is that it creates a disincentive to actually play the game. If I sit down and see that my opponent's list has an advantage over mine or I fall behind in the first few rounds I am likely to disengage to try and preserve tournament points. This is incredibly frustrating for the winning player because it deprives them of the ability to score those 9-10 points they need to make it to the top tables but more importantly it makes the game you are currently playing boring. Who wants to play a match where one player is spending the entire game running away and no significant shots are exchanged? I sure don't!
The second issue is that you can win all of your games and not even come close to placing in the tournament overall. A few years ago I placed 6th at a nationals level competition after I had beaten two people in the top 5! I came up against brilliant opponent after brilliant opponent and all of my games were close. I won with small margins of victory and so didn't score many tournament points. Some of my opponents who I defeated then played an easier opponent and won with a big margin of victory giving them enough tournament points to leapfrog me. My placing in the tournament overall was actually hurt because I won my early matches. A tournament system which rewards players that get matched against poor opponents and punishes players that match against good opponents is not a good tournament system.
The third issue is that someone can score so well in the early rounds that no one else can catch them. This situation normally occurs when the field is mostly comprised of experienced players with a few new players mixed in. If an experienced player is matched with an inexperienced one they can score a 10-1 game. If two inexperienced players also match in round one the outcome of that game can also be a 10-1. In the second round the experienced player on 10 points is then matched with an inexperienced player on 10 points and the experienced player obtains a second 10-1 win. This will put them on 20 tournament points going into round 3. If all the other matches in those two rounds are close it is possible that they end up matched against someone on 12-14 points on the final top table. The result is that unless the 12-14 point player wins really really big there is no way for them to win the tournament even if they win the match. And worse is when the 20 point player is aware of this, chooses not to engage, and lose 8-3 on objectives. The top table doesn't actually have a decent game going on which isn't fun for anyone. The 12 point player ends up placing second after winning 3 games, losing the tournament to someone who they won against on the final table.
I don't know the best way to solve these issues but I have some ideas.
If the tournament point system must be used, the penalty for a loss needs to be identical no matter how bad you lose. If a loss always scores 0 tournament points people won't be inclined is disengage when things go poorly. Instead they will be inclined to fight it out to try and get lucky and scrape out a win. This change will lead to much more dynamic and exciting games because people won't be actively incentivized to run away. The margin of victory brackets will need some tweaking but I don't see that as being too difficult to balance.
If the tournament point system is to be scrapped there are many more options. The simple one is to move to a x-wing style system where number of wins determines placing with margin of victory (or tournament points) being the second tiebreaker. This change will at least stop those situations where you get leapfrogged because people you defeat have easy match-ups and those situations where you go into the final table knowing you can't win the tournament unless you 9-2 or 10-1 your opponent.
It seems to me that the tournament point system was originally introduced because the round length is so long. A long round means less rounds in a tournament. Less rounds means you end up with multiple undefeated players at the end of the day and you need some way of differentiating those players. One idea is to reduce the number of allowed squadrons to 1/4 of your list (an even 100 points in a 400 point game) and also decrease round length by maybe 30 minutes. Less squadrons will result in faster games. Faster games will allow for an additional rounds meaning less undefeated players.
I do not know if any of my suggested fixes are the best solution but I do know there is a problem with the current tournament structure. In my local area people were avoiding tournament play because of this system even before the release drought. Now is the perfect time to fix the tournament system with all the new ships flying around.
If you have any potential solutions to the above issues I would love to hear them.
Edited by Qark