The thing with the prequels is that they really don't have a theme throughout the three films to interconnect them. TPM could easily be deleted and it wouldn't really matter. It does nothing apart from introduce characters. Jar Jars character went nowhere, yet suddenly he is instrumental in voting for the army. We get the clones in ep2 and 3 but nothing to connect them in 1.
So how about a change of plot which will interconnect the three films.? I'm going to give a little snippet of what i have planned.....
Screw the damn trade blockade. It's pointless and boring. It needs some other reason for happening, also with the invasion. So what if the Gungans are actually clones who hold the secret to successful cloning and the trade federation want to get their hands on it (profit/palpatines plans?)? The previous queen made a deal with the trade federation under the guidance of palpatine, to force the gungans to give up the secret. But Padme was made queen and reneged on the deal. Jar Jar could have been willing to hand over the technology but was caught, thus banished. It gives a reason for the invasion instead of being about trade routes. It also helps TPM connect with the next film. But it also gives Jar Jar a different character arc and a sort of redemption scenario when he fights along side his race to defeat the trade federation.
But that's all for now ;)