I haven't started WotBS yet, but I like the story from the parts of it I've read so far. I haven't picked up the last few modules yet. I wanted to convert the whole thing over to 4E and have it become the basis for our next campaign. It will take some time to do obviously, as there are a number of rules and characters that will need to be changed around some. I will also be customizing the modules to fit my group better.
One of the changes I was thinking of making was to change the race of the Ragesians. I know the empire had people of various races, but there are a lot of orcs and half-orcs as written. I want to change that. I'm not sure if I want to go with tieflings or dragonborn (Drakus Coaltongue is *such* a dragony name). I can just picture the authors pointing at their monitors and screaming "Sacrilege!" as they read this.
The trillith don't worry me too much - there's no great need to tie psionics into the game in my opinion. As they stated in the sidebars in several places, if your game doesn't use psionics, just have the trillith use the power of dreams. That's fine by me as mechanically the origin of their power doesn't matter too much.
There are a few mechanical issues I'm concerned about, particularly with the Monastery of the Two Winds. 4E currently doesn't have monks, sorcerers, or low level flying spells. That makes it tricky to modify. I may need to make some sweeping changes, throw out the 3.5 specific stuff, monkey around with the rest, add some powers to kick it up a notch and give some punch to the plotline without getting too long-winded.
Are there other areas or major plot points that are likely to be problematic when converting to 4E? Some of it can just be hand waved, and that's what I expect to do in many places. Several major NPC's need to be reworked completely. I'm not sure what to do with the Inquisitors and all the special counterspell type stuff they do. I don't know how that works in 4E at all. Do those abilities actually come into play much? I haven't read the later modules so I'm not sure I've seen the Inquisitors actually show up, rather than being a distant threat.