just saw the series

I had a similar problem with this chapter as well. It's not that I didn't like the story. I figured the whole "Secret Garden" story was there to teach the Kyo-o (and the viewers) about how adulthood and sex weren't things to be feared or hated, as the Children of the Corn (for lack of a better term) viewed it. Plus, seeing how they portrayed the apocalypse as the Ultimate F---, it made sense they would cover the theme of illegitimate children. And I liked how it followed a coming-of-age structure with the Kyo-o. So she's born in Part 3, and in "The Secret Garden," she goes to "school" (meets other kids, gets her education) and in the last episode, finally reaches puberty. Of course, none of these factors make it a good section of the overall story or make it well-told. Plus, there's no Megumi, no Muhnihausen, and they spent so much time introducing a whole team of characters in part 3, only to have half of them in the next section. I call it a noble failure.
And though I really liked "The End of the Journey," if they hadn't spent so much time on "The Secret Garden," they could've done more with it, or at least made it longer and not as swiftly paced. And, from what I've heard about the making of the series (please don't take this as etched-in-stone fact), I think this was then the production team started having creative difficulties.
My whole problem was the fact that they spend the entire ending of part 3 setting up this part 4 journey, they take to that long, hard Inferno Road and have a total of one adventure. That's it, ONE. Then comes the finale. I liked the story, but I didn't like how they spent two episodes on "The Secret Garden" and only one on "The End of the Journey." And I fully agree the finale was more than a little rushed. I liked the ending, but it as I said before, they needed to spend more time on it, and if they didn't spend so much time messing around in "The Secret Garden," they could have.
No one argues that Urotsukidoji is flawed. But a flawed masterpiece is a masterpiece none-the-less. But rather than excluding part 4, try just going from part 3 directly to "The End of the Journey" and skip "The Secret Garden" completely. It might work better.
And I've said this before, and I'll say it again. This is one of the best, most civilized and fascinatingly insightful boards the imdb has to offer. Nobody has some snotty attitude about their "expertise," nobody acts as though their opinion is the only one that matters, and most importantly to me, nobody thinks that their's or anyone else's taste or views on movies is a gauge of intellect.
To all of you, I raise a glass.

"But, hey, that's me, I could be wrong."