I’m sorry to say but I think your new version turned out for the worse. I liked that you had Obi-Wan and Qui-Gon talking about the Invasion army and watching it through the window, I may not have been clear enough in my earlier comment. What I meant was that you should keep that sequence except go directly from this shot: (https://www.google.ca/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiR0_XEoMbLAhVC0WMKHXryBgUQjRwIBw&url=http%3A%2F%2Fstarwars.wikia.com%2Fwiki%2FFile%3ATrade_Federation_Invasion.png&bvm=bv.117218890,d.cGc&psig=AFQjCNE9lqaAjud6ioE_gbGyMxX4LgoZTA&ust=1458253631320579) to this one: (https://www.google.ca/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwi05JPioMbLAhUE52MKHVpsCHoQjRwIBw&url=http%3A%2F%2Fstarwars.wikia.com%2Fwiki%2FInvasion_of_Naboo&bvm=bv.117218890,d.cGc&psig=AFQjCNE9lqaAjud6ioE_gbGyMxX4LgoZTA&ust=145825363132057 But save the forest part for later. I also think that the meeting scene on Naboo would play better if the last shot was the Queen giving a concerned look.
I agree, I liked that Qui-Gon and Obi-Wan would watch the invasion army come in, but then if I had it like you said where the army immediately invades Theed, the next shot of Qui-Gon and Obi-Wan would have to start with them sitting down at the table, which must be for a considerable amount time given the army has already landed on the planet and invaded the capital city. Like MalàStrana said, it makes both of them look like idiots for not doing anything as the planet is literally being invaded.