By introducing Anakin and Padme as two young people with major formative experiences seemingly enabled by the weakness of the Old Republic (slavery allowed on Tatooine, the Senate’s refusal to stop Naboo’s invasion), The Phantom Menace actually provides what would have been the perfect setup to their relationship and eventual split…except the rest of the trilogy didn’t use it.

Instead of Padme being a fairly generic pacifist type, she and Anakin should both be politically hawkish and support Palpatine’s calls for a stronger executive power. (Hell, Padme & Palpatine were also from the same planet, and the latter was even introduced as an advisor to the former, but nothing is done with that connection other than one line in a single ROTS deleted scene.) This way, the two could bond not just over mutual attraction but also shared political convictions forged by the conflict that brought them together. Then in ROTS, Padme is objective and principled enough to recognize that Palpatine is going too far, whereas Anakin’s views remain clouded by his struggle with the dark side, the Jedi, etc. from the official movie.

Sadly, this reinterpretation couldn’t actually be done with the source material, but maybe it could be made easier to infer by cutting from AOTC Padme’s appeals to diplomacy, opposition to the Military Creation Act (a plot point that should probably go anyway to eliminate the coincidence of the Republic discovering a clone army made just for them at the EXACT MOMENT they’re debating whether to commission one), etc, along with perhaps some creative use of audio from other Natalie Portman roles. Sometimes cutting out obstacles to a particular interpretation is all you need to do to make something click.