You are a fighter level 5, then you get the wish and you get fast healing x.
The DM thinks this is a +2 LA so he gives you enough XP to go to level 7, but you are still level 5. To get to level 6 you need enough XP to go to level 8.
Someday the rest of the party will be +2 levels ahead from you, but you will have your fast healing. If you start with extra XP this day takes a bit longer to come. If not it comes in 2 levels
The only problem is that before someday comes, the rest of the party is without fast healing - which means that your ECL is +2 higher than theirs. However that will happen no matter what, if you get fast healing x.
One solution would be to delete some levels (and the XP too) get the fast healing and have equal ECL with the rest of the party. This benefits you because at higher levels you wont be 2 levels behind (if the LA is +2). Also saves the DM from trying to make balanced encounters.
Or the DM can give all of you something to raise your ECLs.
Okay, let's look at it another way: You get a Wish and you use it to get a neat magic weapon. The rest of the party will some day have weapons of equal ability, as the party advances, but until then he has this big advantage.
So, do you deny him the weapon? Something that is specifically within the power of the spell?
Option 2: He Wishes for some neat ability that gives him an advantage over everyone else, but you don't apply an ECL adjustment. Now he has an advantage over everyone else, and he stay in that advantageous position forever.
To use an example tossed around: Your 5th level fighter gets Regen, which I would call a +2 ECL but we're calling a wash. Yeah intelligent foes can figure out at some point that their weapons aren't really hurting him, and maybe they have enough fire and acid to finish him off. (Although how they guess that without Knowledge Dungeoneering to give a clue is anybody's guess.) Unintelligent foes really stand no chance unless they just happen to have fire or acid as natural attacks.
Option 3: Refuse to let him Wish for anything that gives him a long term advantage.
This seems to be where everyone is heading, but if that's the final decision, why give him a Wish in the first place? Just give him the treasure or spell effect you're willing to allow.
Giving him the power (whatever power he's asking for) may or may not unbalance your game. That's your call. But if you give it to him, don't pretend that you didn't.
The EXP rules go beyond that chart across from the picture of the pretty lady in blue. Keep reading. Exp adjustments are recommended in the sections that follow, based on how much of a challenge the foes really were. If they were given superior tactics, in a situation that particularly favored them, or equipped particularly well, you're supposed to adjust the EXP accordingly. If the party is over-geared, or the situation gives them a particular advantage, you're supposed to trim the Exp award.
If you hand out Exp on an individual basis, the guy who couldn't actually be hurt or killed by the monsters because he had Regen and they didn't have fire or acid should probably take an Exp hit. Why? Because the situation gives him a particular advantage not normally accounted for in the encounter planner.
It may look like an unfair penalty, but it isn't. It's just acknowledging the reality of the game world: Situations are less challenging when you have some inherent advantages, and EXP is supposed to be based on the challenges you face.
Now you can adjudicate this adjustment encounter by encounter, and face the inevitable argument and hard feelings again and again, or you can assign an ECL adjustment one time and be done with it.
You might decide to call it something else, perhaps a "Challenge Adjustment" that doesn't count as actual levels and doesn't require that you add EXP to pay for it, but he's still going to fall behind the advancement curve over time. His new ability lets him coast through some encounters, and when you coast, the others catch up.
It's just that, in this case, they're "catching up" to a head start that isn't really reflected in his actual level, and it feels weird.
I know it's a fantasy game, but pretending that some over-the-top ability isn't going to affect the CR of the individual isn't the kind of fantasy they were talking about.