High HD animals give all of their feats during the LA and none of their stat mods. This creates asymmetries where you get lots of bonus feats through LA rather than class/racial HD.
I propose the animal's regular feats get added as bonus feats during the RHD option of the savage progression. Instead one of the stat modifiers go into the LA side, as well as the size. This avoids the "Run it's a wereboar! Oh, nevermind it's medium-sized, like a baby or something..."
The stat that migrates to the animal RHD should be the highest physical one. We assume that the lowest physical stat has had all the HD stat boosts applied to it. Without the RHD, the lycanthrope doesn't have these. Therefore the lowest physical stat should take a HD/4 penalty to it. These penalties should be reversed as bonii during the RHD.
The smaller two physical stats are available through the LA (including the penalty to the smallest physical stat).
1st Wis +2, natural armor +2, limited alternate form (boar), low-light vision, shapechanger subtype
2nd Limited alternate form (hybrid), boar empathy, damage reduction (5/silver)
Limited alternate Form (Su): ... Until the character has taken one or more levels in the optional bear animal class (see dire boar Abilities, below), changing shape to bear form does not give him the abilities or most of the stats of a bear -- he simply is able to take that creature's shape and size. Since this ability is of limited use, most characters taking levels in the dire wereboar template class choose to take levels of the brown bear class as well in order to gain the full abilities of their animal forms. While in his animal form, the dire wereboar has a -2 penalty or bonus to dexterity.
At 2nd level, the dire wereboar can assume a hybrid form -- a shape between his humanoid and his bear forms. As with the bear form, this change has limited potential unless the character has taken the brown bear class to gain the appropriate abilities. While in his animal or hybrid form, the dire wereboar has a -2 to dexterity and +6 constitution.
The Dire Boar (Lycanthrope) Class
1st 1d8 +0 +2 +2 +2 2 + Int mod. Str +2, alterness, boar abilities, gore
2nd 2d8 +1 +3 +3 +3 2 + Int mod. Str +2, Dex +2, scent
3rd 3d8 +2 +3 +3 +3 2 + Int mod. Str +2, toughness, natural armor +2
4th 4d8 +3 +4 +4 +4 2 + Int mod. Str +2, ferocity
5th 5d8 +3 +4 +4 +4 2 + Int mod. Str +2, natural armor +2
6th 6d8 +4 +5 +5 +5 2 + Int mod. Str +4, Endurance
7th 7d8 +5 +5 +5 +5 2 + Int mod. Str +4, natural armor +2
Wereboar Bonus Feats: The wereboar gains the feats indicated as bonus feats, assuming that he doesn't already have them. If the wereboar doesn't meet the prerequisites (if any) for a bonus feat, he gains the feat but cannot use it until he does meet the prerequisites.
So does this help? Or do you love those Legendary Tiger feats too much?