I'm seeing and find myself agreeing with both sides of the coin.
I love the idea presented by the OP. It reminds me of Lost Caverns of Tsojcanth which came with an entire second "module" practically, just of the "new/unique" monsters, new spells, magic items, etc. Practically a whole mini-Monster Manual just for that module.
Throw in a few individual NPC creations with unusual theme and/or background combo's (like the Pirate Wizard, someone mentioned up thread) which can be used whole hoc as an NPC(s) but also understandable/usable for a potential PC creation...maybe an "optional rules module" for something in the adventure that hasn't been covered in the DMG (or just a different optional way of handling something that has been covered in the DMG).
I don't know about whole "new" classes, but a combo of class/race/theme that might not be readily evident or meet a whole separate archetype of their own and/or optional rules modules that one can easily incorporate or ignore would work for me...and I think we're definitely on to something.
Not every adventure module, certainly, but the occasional "here's an extra buncha pages with some idea stuff you might not have seen yet." LCoT style.
Yes, almost certainly, the monsters, spells and magic items will find their way into being re-published in a themed splat book, MM2, Complete Magey Mage Stuff Handbook or something at some point. But that doesn't strike me as a reason to dismiss the whole idea. The Bodak, the Behir, the Pech and Derro, the "Forcecage" spell, (even "Valley Elves", I think, iirc) etc. were all in LCoT before (or maybe "along side" for some of them) we ever saw them elsewhere.
That said, I also see the convenience and interest of splat books in general. Having everything you might need to reference on a particual topic in one place is certainly useful. I, personally, do not buy them often/have many myself, unless they are a theme/collection of topic I think I'll like or want to use...which I assume is how most people do their shopping.
So, I think, the "argument" here is pretty...moot. There's no reason not to do/we can't have both...extra tidbits built into adventure modules and separate whole splat/theme/topic books.
--Steel Dragons