Absolutely agree with so many of the points here. Great example, this one:
I had exactly the same problem with that damn quest. The biggest issue, I think though, is inconsistency. Sometimes the journal can be ignored except for reference (if you've got a list of ingredients to collect, say), which is the way I, and I'm guessing most people here, would prefer it. Other times, like the above, it worms its way into the actual quest structure. If the latter were consistently true, I wouldn't like it, but at least you'd know what to expect.
Better thinking about quest design can eliminate even the reference use, in fact. Many of the best mod designers, like David Brasher, simply issue the PC with a note or scroll they can consult and discard whenever they choose. Coupled with a disciplined use of pop-up boxes (though I'm guessing that these are widely hated too) you might not need the journal at all - well maybe just to remind you of outstanding quests. One thing mod authors are guilty of here, though, is not labelling these well. I find too many 'faded'/'scribbled'/'short' etc etc notes in my inventory, not to speak of just 'Note'. The vanilla game actually does a much better job of this.
As for the journal (or pop-ups) telling you your feelings and motives, that's truly awful and could actually be modded out. It's surprising no-one's done so. (Though I can think of one case where it can be justified, and that's alternative start mods. Used properly, of course.)