Despite the placement/usage of embers and such I don't think there's an intended order with the Lord Soul bosses, personally.
The only area that seems up-in-the-air to me, regarding From's intentions, is Darkroot (whether you go there before or after Sen's/Anor Londo).
I think The Catacombs are put where they are to torture new players and reward repeat players. Or maybe the reason they made Pinwheel so easy -- despite the fact that he drops the 2nd most important item in the game -- is so the rare noob who has the patience, skill, and intellegence to run The Catacombs early is rewarded appropriately. I kinda doubt that though, as you'd have no way of knowing about the need for a divine weapon yet, and unless you got REALLY lucky and made your way to the first necromancer you wouldn't know about that aspect of it. Actually, I suppose Demon's Souls vets could figure that part of it out, I guess.