Well one of the problems is that FitLucario00 should not be renamed.
FitLucario00.pcs is the model data (so in this case everything that is Mewtwo's model is in there) along with FitLucario00.pac
FitLucario.pac is the data for the attacks
You should have at least 4 files in the Mewtwo one
FitLucario.pac
FitLucario00.pac
FitLucario00.pcs
FitLucarioMotionEtc.pac
You can use just the FitLucario.pac file but it will still be Lucario using Mewtwo's moves with Lucario's animations
You shouldn't be renaming any files for the Mewtwo one at least
Also do you have the right codes uploaded to Gecko? If you don't have the right code file in your SD card then Gecko will load the game but it won't change anything about it. Make sure you have the right code file.
Thank you, a informed, smart answer for one of them.
Aside from that I wouldn't know what your problem is.
Hey, at least you replied and tried to help, right?
EDIT- Oh also one more thing is to make sure you have the files in the right folder. For Mewtwo your SD card should look something like this
Root->private->wii->app->rsbe->pf->Fighter->Lucario
Since it's NSTC-U, shouldn't it be rsbe01? Also, like this?
Also Root is just the normal root folder of your card you shouldn't actually have a folder named root in there
I know, I did put it in the root, I learned some time ago that "Root" meant in the main spot.
Code files go into Root->codes and it should be named RSBE01.gct
Did that.