But, when people talk about taking out the entire pod race, or taking out all references of gungans, or completely removing the Yoda vs. Dooku lightsaber duel, that would disturb the flow of the movies even more rather than smooth the flow. I just have the feeling that those sections would just be too big to lop off effectively.

But hey, I could be wrong. ;)

No offense, but I think you are. ;)

I've seen large portions reedited brutally and whole sections cut with only positive effects on the story. You'd be surprised what can be cut. I thought the same as you until I saw an ep3 edit with no Yoda/Palpatine duel. As bad as it was, I thought that needed to be there intercut with the Obi-Wan/Anakin duel. Not the case, as it turns out. The film even flows better without it.

There are a lot of moments like that. Sometimes I wonder if you need episode 1 at all, apart from, like, two or three scenes. TMBTM's silent edit is two and a half hours long, and yet most of the story elements are intact (still too many, imo!), even with approx. five hours cut.

EDIT: Honestly, I don't really think the story elements are that good either. It's way too political. Not that there's anything wrong with a political story, and I dig Roman history (an obvious influence) as much as the next guy, it just feels awkward and uninteresting to me. Not to mention unexciting. We're used to Han Solo, now we get political drama delivered in costume drama stylings, with interminable preachy speeches in pretty badly written and too ornate language. But it's not just the writing. The ideas are bad too.