The racial HD / level adjustment scheme never worked. Kludge fixes like savage progressions only smoothed out the pain, didn’t really fix it.
I suggest that you attempt to make lycanthropy power-neutral, so that it can be applied to players without making things too problematic. Here’s my suggestion:
Afflicted Lycanthropy
Afflicted lycanthropy is an acquired template that can be added to any humanoid or giant (referred to hereafter as the base creature). Afflicted lycanthropy also refers to a creature of the animal type, known hereafter as the animal, which must be a predator, scavenger, or omnivore whose size is within one size category of the base creature’s size.
Size and Type
The base creature’s type does not change, but gains the shapechanger subtype.
Hit Dice and Hit Points
As the base creature.
Speed
In normal and hybrid forms, as the base creature. In animal form, the afflicted lycanthrope gains the movement modes of the animal.
Armor Class
In normal and hybrid forms, as the base creature. In animal form, the afflicted lycanthrope gains the natural armor of the animal, but loses the ability to wear armor.
Attacks
In normal form, as the base creature. See animal form and hybrid form, below, for details on those forms’ attacks.
Special Attacks
In normal form, as the base creature. See animal form and hybrid form, below, for details on those forms’ attacks.
Special Qualities
Alternate Form (Su)
The afflicted lycanthrope gains two alternate forms, known as hybrid form and animal form. Changing forms is a standard action.
Each form replaces the racial features of the base creature’s race, including racial bonuses to ability scores. An afflicted lycanthrope that qualifies for feats or prestige classes in its normal form does so in its hybrid and animal forms as well, even if the loss of racial features or the application of penalties from those forms would ordinarily disqualify the afflicted lycanthrope.
In the case of races that grant bonus feats, these bonus feats are retained, but the afflicted lycanthrope cannot use or benefit from these bonus feats. Any feats or prestige classes that require these bonus feats continue to function (the afflicted lycanthrope still has the feat, simply cannot use it) unless they rely on the use of a bonus feat directly (e.g. if the base creature had Deflect Arrows as a bonus feat, it would retain their Snatch Arrows feat that relies on it, but could not use it because using Snatch Arrows requires using Deflect Arrows).
A slain lycanthrope reverts to its humanoid form, although it remains dead. Separated body parts retain their animal form, however.
Afflicted lycanthropes find this ability difficult to control (see Lycanthropy as an Affliction).
Animal Form
The animal form of the afflicted lycanthrope is identical to a druid using wild shape to become the animal, except that the afflicted lycanthrope loses their racial features as noted above. An afflicted lycanthrope is not limited in either duration or frequency of taking on its animal form, as a druid is, but again, as noted above, afflicted lycanthropes can have difficulty controlling the ability.
Hybrid Form
The hybrid form of an afflicted lycanthrope is a mix between the base creature and the animal. The afflicted lycanthrope has its ability scores changed by hybrid form, and gains natural weapons.
Ability Scores: In hybrid form, the afflicted lycanthrope gains ability score bonuses based on the animal’s ability scores. If the animal has Strength at least 4 higher than its Dexterity, the afflicted lycanthrope gains +2 Strength and −2 Dexterity while in hybrid form. If the animal has Dexterity at least 4 higher than its Strength, the afflicted lycanthrope gains +2 Dexterity and −2 Strength. If the animal’s Strength and Dexterity are within 3 of each other, the afflicted lycanthrope does not gain adjustments to those ability scores.
If the animal has Intelligence 1, the afflicted lycanthrope receives a −2 penalty to Intelligence and +2 to Wisdom or Charisma, whichever is higher for the animal (if tied, the afflicted lycanthrope chooses which ability score receives the bonus upon being afflicted; once chosen, the choice cannot be changed), while in hybrid form.
If the animal has Intelligence 2, the afflicted lycanthrope may choose to take the changes to mental ability scores while in hybrid form, as if the creature had Intelligence 1, or not, taking no changes to mental ability scores.
If the animal has Intelligence greater than 2, the afflicted lycanthrope gains a +2 bonus to Intelligence and a −2 penalty to Wisdom or Charisma, whichever is lower for the animal (if tied, the afflicted lycanthrope chooses which ability score receives the penalty upon being afflicted; once chosen, the choice cannot be changed), while in hybrid form.
Attacks: The afflicted lycanthrope gains, in hybrid form, natural weapons similar to those of the animal.
If the animal had a pair of primary natural weapons, the afflicted lycanthrope in hybrid form gains a pair of natural weapons of the same type. The afflicted lycanthrope’s version deals 1d6 plus their Strength modifier in damage (for a Medium afflicted lycanthrope), regardless of how much damage the animal’s did.
If the animal did a single primary natural weapon, the afflicted lycanthrope in hybrid form gains a natural weapon of that type that deals 1d8 plus 1½ their Strength modifier in damage (for a Medium afflicted lycanthrope). This counts as a two-handed weapon for the purposes of Power Attack and similar.
If the animal had both sorts of primary weapons, the afflicted lycanthrope chooses one when afflicted. Once chosen, the choice cannot be changed.
In hybrid form, the afflicted lycanthrope may continue to use manufactured weapons.
Low-light Vision (Ex)
A lycanthrope has low-light vision in any form.
Lycanthropic Empathy (Ex)
In any form, lycanthropes can communicate and empathize with normal or dire animals of their animal form. This gives them a +4 racial bonus on checks when influencing the animal’s attitude and allows the communication of simple concepts and (if the animal is friendly) commands, such as “friend,” “foe,” “flee,” and “attack.”
Scent (Ex)
A lycanthrope has the scent ability in hybrid or animal form.
Base Save Bonus
As the base creature.
Abilities
In normal form, as the base creature. See the animal form and hybrid form entries, above, for more details on how those forms affect ability scores.
Skills
As the base creature.
Feats
Generally, as the base creature. Creatures who gained bonus feats as racial features lose those when in animal or hybrid form. See the alternate form entry, above, for more details.
Level Adjustment
+0.
The ability to switch into animal form can be useful, and low-light vision, scent, and empathy are always active, so there are upsides to this template. They’re fairly minor, however, and the removal of racial features ensures that the alternate forms are not that great. The issues controlling the transformation, I think, cover those advantages well enough to consider this a power-neutral-ish template.