In my game I abolish LA, and give RHD equal to approximately CR+0 to CR+3. I factor in stat boosts and minor and major abilities. As a rule of thumb, one RHD can "pay" for about 6 points of stat boosts and a minor ability. For major abilities, such as casting, you will need a full HD. I do not take into regard, however, the general consensus that bonus is worth more than penalty.
To give a few examples:
The Aranea from the SRD casts as a third level Sorc, IIRC, and has +18 to stats (if you give it full PB, which is another matter), plus some shapechanging abilities. It's also CR 4. First rule would put it at 4+ 1 to 3 RHD. Rule of thumb says about 3HD for casting (full casting levels which stack with later class levels), then three HD for abilities. So you get a 6 HD critter with 3rd level sorceror casting. And then you handwave it, how would it compare to a 6th level sorc gish (which it would be forced to play)? So basically I say, would I play it as a 6HD critter? Probably not. But five, maybe. So I give it five RHD and third level casting that stacks with later Sorc levels.
Obviously it depends on the power level of the party.
There is another method where you don't give the guy a full point-buy, but instead give monster stats adapted via NON-Elite Array. That's equivalent to a 15pt point buy. Now you deduct stat boosts and can adjust the RHD. This is easier if you use non-standard buys without escalating costs, because then you can adjust one for one: For instance a 30pt non-escalating point-buy would give leave that critter at +3 points over the normal PC, at which point you lose another RHD and make it playable as a 4HD critter. (3 casting, +3 abilities,+some minors, that about fits +1.)
Another SRD example is the Lammasu: CR8, 7 levels cleric casting + some SLAs, plus stat boosts.
Method 1: Use monster stats and about 9 RHD, this is what I suggested to an applicant in my game once.
Method 2: Point-buy and about 6 extra HD (for +36 abilities) (on top of the 7 for cleric casting). This clearly doesn't work, because at that point casting is too far behind. However, I would be careful with reducing them too far. At least +3-4 are warranted. A lot of martial cleric builds lose 2-3 levels of casting, and this guy still has mad stats, even without the fancy class features of the martial clerics (RKV for example). So you're trading abilities for class features, which from a brute force perspective works quite well.
In both cases don't forget that those RHD are of a fairly good type, so these characters will come out strong.
EDIT:
Something I forgot earlier: One important thing to note in all cases is role of money in the equation: CR doesn't assume that a critter has equipment worth its WBL, while of course characters DO. WBL plays a huge role in character power, while most monsters are made to compete without magic items whatsoever. Often enough, if you were to give a monster of CR X items with value of WBL for it's (original) CR, then you could easily add a few digits. Likewise, strangely enough, I guess it's pretty rare that you get a kill an enemy character with WBL for his level (because that would provide far more than EL appropriate money), but characters still get CR=level.
It would be interesting to try playing monsters with CR=ECL without giving them money to start with.