First, let me once again thank Nilus and Nix for running great events. I had a blast. Overall, I have no major complaints. As my family and coworkers will tell you, that's very rare... so take it as high praise.
Time limits on the event - The rounds could have been slightly longer, but if they're too long then you increase the likelihood of player burnout. Players should enter these events realizing that they need to play quickly and score/secure VPs as early as possible. I do not recommend taking Avatars in this type of format (I didn't manifest an Avatar all weekend).
Terrain - In addition to the reasons you stated, it's important to remember that the hall is open throughout the duration of the convention. If elaborate (i.e. expensive) terrain is used, it might disappear during the night.
Single Elimination - Single elimination is perfect for the final day. Swiss tournaments can result in two (or more) players with the same W/L ratio; Single elim allows for a clear winner.
Declaring your Master - I loved this. I hope it becomes standard practice. Especially when playing against Outcasts, it was a relief to know what master I was facing before picking out my crew.
Adjusted Destroy the Evidence - I liked this a lot. Collodi is generally able to secure a VP on the first activation; this made him wait an extra turn. It actually let me fill Collodi with stones first turn (normallly I would make my dolls fast so they could destroy the middle evidence marker). Speaking of which, I liked that there wasn't a middle evidence marker; it made the tactics of scoring VPs far more interesting because the players had to head toward their markers while trying to keep models near their opponent's markers. This was one of my favorite games of the weekend.
Changes to Treasure Hunt - Normally I would take Collodi (with either Zoraida or Lilith) without blinking because he and his Marionettes can grab the counter during their first activation. Since it couldn't be picked up until the second turn, I decided to take a crew that I much prefer: Dreamer. It was my only loss on Saturday (Mr. Weakland won), but it was still fun. I liked getting a VP for just picking the counter up once.
Terrain Density - MUCH better than last year. As others stated, my spirits had a fine time with it while some more "traditional" models had trouble. Some people were complaining about the lack of firing lanes; they should remember that Malifaux is a very melee-oriented game. Models often need to get in their opponents' models faces in order to score VPs. By the way, Von Schill made plenty of long-range kills during the one and only game that I took him.
Terrain Types - There were some structures with only one door, and some without any doors. A bit more care could be taken in constructing these. If nothing else, take a pair of scissors to some of the walls to create openings. I liked playing with more buildingy-looking buildings on Sunday.
Scoring - Perfect; this is the best scoring method, from my point of view. That being said, I like formats that award tie-breakers based on strength of schedule, but this can be burdensome to calculate and implement fairly.