Haven't tried this hack yet, but when looking at the documentation, you seemed pretty cosistent at neglecting the legends. I have some suggestions:
-Please swap Articuno's special stats. It deserves to have a high Satk just like the rest of the trio (the special split in GS was a mistake and has been caried over to more than 10 games, which sucks).
-The birds deserve Work Up. The non-legendary birds get it, so why not the legends?
-You can enable the three special purification moves as lv1 moves on the trio, just like you did for the event moves on Entei/Raikou/Suicune.
-Make Crunch available all legendary beasts. I suggest moving their Elemental Fangs to lv 1 (getting rid of Leer or Bite) and putting Crunch at lv 50. (Raikou can gain Electroball at lv 43, for instance)
-You can also give them Moonlight at lv 78, as they are based of nocturnal animals. (Calm Mind is a TM anyways)
-Superpower has been underdistributed among the legends. There is no way Palkia, Groudon, Entei and Ho-oh cannot learn this move.
-The Regis have no secondary ability. I'd give them Analytic, as they really deserve it, more than Metagross (I'd rather give him Sheer Force).
-Actually, having two abilities on a legendary is sort of a crime aestitically. Just leave them with the best one (they don't have to have Pressure, for instance).
-I'd redo the level sheme of Dialga/Palkia/Giratina. Ending at level 50 is nothing for a legendary and it requires lots of moves to be learned by the move relearner (not sure what they were thinking in HG/SS...).
-Palkia learns Aqua Tail twice. Fix that! I think he deserves Aqua Jet in his moveset.
-Reshiram/Zekrom deserve Hammer Arm. They don't need Slash...
Obviously, this is my opinion. Maybe I just should make a hack myself, although I have never done that. If these suggestions get rejected by other's comments, you'd better ignore them entirely...