With its smaller color pallette, I'm not sure how well the PCE would do replicating the soft watercolor pastels while maintaining color count. Besides that, it looks like much of the game could be done by modifiying the foregrounds and backgrounds to better suit animated background tiles, strip parallax, and overlapping foreground sprites; it wouldn't be anywhere near pixel perfect, no, but nor would it need to be perfectly flat and missing the parallax altogether.
A few other things I don't know about:
Fade In/Out Cut Scenes: in the opening, it fades out the old scene while fading in a new one overtop the old, all the while with text in front of both. I assume it's using sprites for text and fading in and out the two background layers separately, but how could you replicate that in PCE? Keep the text as sprites and animate the background with lots of tiles?
Flames: probably not doable without a second layer for 'em to ride in, but who cares? They're ugly! At first glance they look kinda neat, but then you realize it's a short animated loop, non-transparent, and doesn't scroll. You'd lose that extra layer of depth, but methinks it'd look better with the background tiles themselves being animted to show the buildings aflame.
Rising Water Transparency: could it be done with palette tricks like the water drain in Lords of Thunder? Hell, maybe that's what the SNES game is doing anyway, rather than real transparency.