Carrying the recent flurry of PT ideas over from the ANH:R thread it shouldn't be impossible to create another pupil for Obi-Wan using the existing material.

Here's one possible remedy.

Make Obi-Wan in TPM a fully trained (by Yoda) Jedi paired with Qui-Gon for the duration of the Naboo crisis.

Make Jango Fett, Boba Fett.

Take the footage of little Boba and place it in silently in TPM in the Temple scenes and shift the dialogue aimed at Qui-Gon about not being able to have another apprentice to Obi-Wan.

Have Obi-Wan take on Anakin and have his former pupil give Obi-Wan dirty looks as he is led away to be taught by another Jedi Master.

Have the Vader persona manifest as soon as Anakin loses his mother.

Cut the actual scenes of Anakin killing the sandpeople but have them appear as dreams so Anakin and the audience feel he wanted to do it but didn't or maybe he did but blocked it out (Padme could admit love for a man who to his shame admits to wanting to kill the people who caused his mother's death but a child murderer?).

Have some of the Jedi killed by a mysterious hooded figure before Anakin's supposed fall (Vader begins as Hyde to Anakin Jekyll but we don't know that yet we have no idea who this hooded guy with burning eyes is).

Show Anakin race to the Senate building during Windu's fight with Palpatine and have Windu killed by this shadow figure.

Don't show the face on the hologram of the Sith naming of Vader (it could be that little boy from Episode One).

The fight on Planet Hot-Hot is the real problem as is Padme's death.

As someone not liked by the new Emperor and the mother of a Jedi's child/ren it would make sense that the remaining Jedi would want to hide her so maybe she dies alone and unremarked on Alderaan while one of her decoys gets a state funeral in ceremonial make-up.