I agree with you about spreadsheets being used where databases make more sense though.
* Calc's pivot tables is clunky, while working on Excel 2010 is like working on butter with a hot knife. No, it's not a "getting used to" thing.
* Basic stuff like filter/sorting tools: Excel has a far better flow that helps you get the job done faster
* DataNitro
* Charting in libreoffice is broken. I use ggplot for most of my day jobs, but sometimes when you need to pull up a quick chart, LibreOffice serves to only nerf your speed. Again, not one of those "getting used to" thing
* Try pivot-tabling a 1M row csv in Calc.
* VBScript (though that's now more and more subplanted by DN)
* Analysis tools - Excel is just so much richer.
These things LibreOffice is better than Excel:
* CSV (excel's a little clunky with CSV import)
* regex search
EDIT: formatting
Anyway, I agree with everything else you said, it matches exactly my experiences with Calc.
That being said I'd prefer Apple to push their iWorks applications over better OOffice - their technological basis is by far the best - the outcome of each click and each edit is completely predictable, the whole rendering engine works consistantly across all three products, so do hotkeys. They're just lacking a lot of sugar on top like the features you mention.
Google Docs and Presentations are good enough - there is simply nothing close to Excel and VBScript.
note: by this i mean interoperability more than anything else.