So, I finished watching Epsiode I - Path of the Padawan:

First of all, i lift my hat. Really great work. The story per se flows insanely good, I personally never got bored, right amount of humor left. I am happy.

I have some minor issues. You already stated that you’re aware of some unfortunate transitions here and there. So my observations:

opening crawl
did you use the right angle for the floating text? It seems off. Also the text disappears to fast, let it fade more. If necessary use additional footage for a transition from the floating text to the space or a new scene
Obi-Wan and Anakin fighting Ventress
it is obvious there is footage missing e.g. as ventress is Running up the stairs and the next shot is, that she’s sitting and lurking both to come closer. Add footage back in.
0:51:11
Beforehand they talking about to go to a council meeting and than there is a cut to an mission briefing. I’m afraid this don’t work, you’ve to add the council meeting.
1:12:04
Anakin told the clone to make the ships ready, to be prepared if obi-wan asks for their help. You should add his call for help, because it is strange to see Anakin and Ashoka at the medical station and in the scene afterwards onboard of the ship. The same counts for master plo koon. The transition at 1:12:57 is too hard, somehow make it smoother.
1:12:32
did you do some kind of color correction? If so, the whites are too bright
1:34:12
the cut to the new scene is also too hard. Add footage of obi-wan, anakin, padme back in and make the transition smoother
1:54:59 to 1:55:00
again, the cut is too hard, add source material and fade smoothly

Anything else is fine and works well, from my perspective

Some other questions:
Which application do you use for editing? Is it possible for you to do 1080p? Could you render with less compression, so the files will be bigger but contain more quality (e.g. up to 10 Gb per episode) and use mkv as target file?