An older Anakin and younger Qui-Gon are both great ideas, and both would have probably lead TPM - and by extension the rest of the PT - to being more faithful to the OT.
I don't see how a shapeshifting Jar Jar could be an improvement, though. If anything, it would have only made him more annoying.
As for the stuff with AOTC, none of the stuff mentioned would have made any significant improvement to the movie; it would have been just as bad, but in a slightly different way.
Though I do like the idea of Padmé pulling a knife on "evil" Anakin, it wouldn't have made her any less of a cognitive dissonant, racist ditz.