(For example, if it were up to me I would've of course combined Qui-Gon and Obi-Wan into one character -- but I also would've combined Jar Jar and Anakin into one character, or at least given the role that Jar Jar has in the story entirely over to Anakin.
It's not a bad idea, but I think you don't need to make such dramatic changes to make things better. In order to give a more central role, you make him the harsh and impetuous one, and you make Qui-Gonn his quiet and conservative master. That way, Obi-Wan becomes the protagonist of the movie, every plot element falls into place, and it creates an interesting dynamic in the next two episodes, where Obi-Wan has to become the Master of someone who is even more frantic and free-spirited than he is.
As for Jar-Jar, once you realize that he is the Han Solo character of the movie, the outsider who guides our heroes through enemy lands and who's not entirely convinced by their mystical mumbo-jumbo, you understand that you don't have to change him that much to make the character work.
Or you make Anakin the conservative, within-the-rules type as compared with the more free-spirited Obi-Wan. That seems better to me, as Anakin is (even in the actual PT) sort of a fascist.
And the thing about Jar Jar is that in the movie, even though he has some aspects of the Han Solo role he is primarily C-3PO. Trying to make him too much of a Han leads back to the character redundancy thing again (as the Jedi are our action heroes). But eliminating his character and substituting Anakin could be a way of getting around that.
As for Qui-Gonn and Amadala, they really do have no personality in this film. We are told nothing about their back story, their opinions, or their likes/dislikes. That is how we get to know a character. Every line of dialogue given to these characters relates to the plot or what is happening on screen.
Compare this to what we find out about Han just in the first film. By the end we know that 1. He's a rogue who is mostly interested in money, but goes through a character arc in which he is willing to risk his own life to help Luke. 2. He's proud of his ship, which is almost a separate character entirely, and has an extensive history with it. 3. He doesn't believe in the Force, and doesn't really care what others think of him. He's confident, but not to the point where it becomes a detriment.
At the end of TPM, what do we know about Obi-Wan. 1. He's a Jedi in training. 2. He's loyal to Qui-Gonn, and gets mad when Qui-Gonn is killed. That's about it.
QUI-GON:
- He's unconventional, prefers to do his own thing.
- He's always two steps ahead of everyone in planning things.
- He's always calm and centred, possibly as a result of being a Jedi Master for so long.
OBI-WAN:
- He's conservative, conventional, a bit stuffy and overall very orthodox as a Jedi.
- Yeah, we actually don't know much else. Obi-Wan is criminally underused in TPM.
AMIDALA:
- It's notable that this character is INTENDED to be a bit of a mystery. We're not even supposed to notice the double-switching.
- When her homeworld is invaded and she's whisked away she feels everything's slipping out of her control. Qui-Gon's basically taken charge, and when she goes with him on Tatooine to try to keep a rein on him he blatantly ignores her:
Amidala: "Are you sure about this? Trusting our fate to a boy we hardly know? ...The Queen would not approve!"
Qui-Gon: "The Queen doesn't need to know."
Amidala: "Well... I don't approve!"
- Going back to Naboo and enlisting the Gungans' help is her idea, her plan, so it's basically her taking charge and asserting her authority again.
- I will say, though, that again the character is underused after the "Amidala is Padme!" reveal. I'd say this is due to the four-part action climax.