With total restructuring I think it could be made at least as good as ROTJ (the current form), if someone were to throw some serious money into shooting some new scenes I think it could be better still.
First of all we need a character to follow and to be honest the only one who really fits the bill is Padme/Queen Amidala.
Anakin is too young and only comes in half way.
Qui-Gon is too inscrutable, Obi-Wan is too underdeveloped.
The Queen is under heavy make-up most of the time so it might be possible to expand her role by finding someone a bit Portman/Knightly shaped and obscure them in costume and make-up.
The whole film hinges on the Queen liberating her people.
You have her trying to get satisfaction through the Senate and the bureaucrats. You have her trying to take matters into her own hands and having her ship shot down. You have her (in her handmaiden guise) taking an active role in trying to get the ship working again and meeting Anakin. You have her coming up with the final plans to kick the Neimodians of her world.
I had an idea last night that might help too.
One of the criticisms highlighted in the review we must have all watched now was the problem of the four concurrent conflicts being too much too late.
Nute Gunray could stay on his ship until he was convinced of ultimate victory.
The Gungan vs Droids battle could be a ruse (they could deliberately surrender at a key point creating the impression that the crisis is over).
Once the droids have appeared to have won he could land giving the Queen her chance to use her familiarity with the palace to capture him.
This would isolate that battle from the action making it a prelude to a more easy to handle three part ending.
Padme in the palace. Anakin (who has 'borrowed' a fighter and is deliberately in the air using his raw abilities to take on the blockade fleet (not just one ship) and the Jedi on the command ship trying to shut it and the droids and signal for help, only to get caught in a fight with Maul ship's reactor halls.
I've said it so many times but the going back and forth in the current version is a major problem with TPM.
Just as destroying the Death Star was the main aim of ANH removing the invaders from Naboo should be the main focus of TPM.
Do we really need to see Anakin being tested on Coruscant?
Do we really need to see Padme on Naboo at the beginning or have Qui-Gon and Obi-Wan in the Gungan City?
Start on Coruscant, get shot down and have to land on Tatooine and then go to Naboo.
And start with a big bang.
Have the Naboo launch most of their fighters at the Blockade and have them shot down and their communication satellites destroyed.
That way the senate could be bogged down with figuring out what to do with no clear information coming out and the Jedi could be concerned enough to send a couple of their own to investigate.
Change the motive of the Trade Federation to reclaiming a planet they had a prior claim on (which explains why the native Gungans don't like the Naboo).
And redub all the silly characters so they have proper roles to play (Jar-Jar the token Gungan representative despised by his own people for mixing with Naboo is much more Star Wars than a clown rabbit with a racially offensive patois).
I'd even redub Jake Lloyd so what he does say comes across a less annoying.