I don't like the effect of LA in 3.5e, but I think the PF system kind of tossed out the baby with the bathwater.
So with that in mind, here are some ideas:
LA as negative levels:
Pretty self-explanatory. +2 LA means you have 2 negative levels, which cannot be bought off. (-10 hit points and -2 on most checks) This is painful, but you still have your spells, class abilities, and advancement on par with the rest of the party.
LA reduces starting ability points by -8 per LA. This is a very direct handicap.
LA buyoff:
Most racial HD are worth 'less' than PC classes. This buys off LA at different rates.
-1/2 LA per HD: Animal, Construct, Fey, Humanoid, Plant, Undead
-1/4 LA per HD: Magical Beast, Monstrous Humanoid
Under normal LA/ECL model, you earn HD two at a time with the first list. That is, a character with 4 Humanoid HD and +2 LA has an ECL of 6; 2 more Humanoid HD buys off one LA, so becomes 6 Humanoid HD and +1 LA / ECL 7.
Under the '-8 points per LA' model, you gain 4 points back per racial HD (but such points are still limited by chargen rules). At DM's option, you can even earn a net positive point value; you're essentially trading class abilities away for having bonus points.
If you want to calculate what the 'true' LA is of a monster (looking at 3.5e numbers), you can trade racial HD back in for LA. That is, an ogre has 4 Humanoid HD and +2 LA. It's 'real' LA is +4. This can be useful if you go with a different LA scheme and don't necessarily want racial HD.
Another idea, based on similar principles and more 'PF friendly.'
For Aberrations, Animals, Constructs, Fey, Humanoids, Ooze, Plant and Vermin:
Take the lesser of: HD, half of CR (Rounded down).
Subtract this value from CR and subtract twice this amount from HD
If HD is no more than twice CR, this will equalize the two.
For Magical Beasts and Monstrous Humanoids:
Take the lesser of: 1/4 HD, 1/4 of CR (Rounded down).
Subtract this value from CR and subtract four times this amount from HD.
If HD is no more than four times CR, this will equalize the two.
Example:
Ogre: CR 3, 4 Humanoid HD
Lesser of 4, half of 3 CR or 1, so ‘1’.
Ogre becomes: CR 2, 2 Humanoid HD. The ogre is treated as a 2nd level character.
While I don't agree with Paizo's CR = level equivalent idea, this is consistent.
The ogre trades away 2 levels of fighter (+2 hp, armor, fighter abilities, feats) or 2 levels of barbarian (+4 hp, some armor, skills, rage, etc.) in exchange for a big boost to (some) stats and permanently/undispellably Large size. (Note that you can have permanent Enlarge Person cast on you for about 3k or so)