Wow, lots of interesting stuff here.
--The file is mirrored. If you pay attention to the character trophy list, going in the correct mirrored order, left to right, top to bottom, the hole in the character trophy list is exactly where the Ice Climbers should be according to Melee and Brawl's internal character ordering.
--As mentioned, Tharja is conspicuously missing. ESRB probably told them to remove it.
--There are some trophies from disparate series that are mixed in with other series--these are probably holes in the series list that were later filled in by others. Like Dunban is where there should be a Sonic character.
--The first listed non-playable Pokemon trophies are Pokemon Trainer, Squirtle, Ivysaur, Mewtwo, and Pichu, in that order.
--The Assist section is funky. There is a conspicuous hole between the Sablé Prince and Riki. Barbara Bat, a ReDead, Doc Louis, a 3D Excitebiker, and the Ice Climbers (!) are listed in the Assist Trophy section.
Interesting stuff.