The protagonist is meant to be the needle that guides us through the thread of the story.
Anakin doesn't turn up until more than a third of the way through the story and is absent for much of the action that takes place even after we meet him.
Even if you can channel yourself into the mind of this largely featureless place holder of a character you can't use him as a guide to what is happening in this story.
Luke in the PT may not be physically present in every scene but is largely the focus from ANH through ROTJ.
The nearest thing we have to a protagonist is Padme in TPM.
The struggle of the film is largely hers and Anakin is as much a secondary character in that story as Qui-Gon or Palpatine.
Sadly there isn't much development of her character, she hits one tone throughout.
If she started out as someone willing to defer to mechanisms of the Republic but then come to lose faith in it and take matters into her own hands her path would have been similar to Luke's (willing to defer to his Uncle's demands until events allow him to stand on his own feet).
The bare bones of that are there but it's not worked on and actually undermined by the hamfisted deployment of the decoy plot device borrowed from The Hidden Fortress.
The film needed a re-write.
The sad thing is most of the elements could have made for a very good film with a bit of re-shuffling and merging Qui-Gon with Obi-Wan to make a single character with more depth.
Re-editing can nudge it a bit nearer to being a better film but really only remaking the thing can really save it.
The tone is way off too.
We really don't feel that Naboo is suffering or that Anakin and his mother aren't better off as slaves (which is a big mistake).
If Anakin and his friends were kept as Pod jockeys (because of their size) it could explain why his life as a slave doesn't seem superficially so harsh.
The threat could then have been from being forced with his friends to race until they ultimately died in the arena.
His mother and the other adult slaves could be breeding stock for producing other racers and if he was lucky enough to survive his childhood of racing he could become a trainer (still a slave).
That would have made sense of the slave quarter.
Having a pod race where the racers were either small aliens or other children would have added a darkness to the podrace on par with the murder of Owen and Beru.
Sebulba as another human child and a rival to Anakin would have been much more interesting especially if the character turned up later as rival student in the Jedi Temple (thus intensifying the Vader revelation in ESB).
At least in Indiana Jones And The Temple Of Doom (for all it's many flaws) child slavery is made to be the horror that it is.