Capable SP Admins/Consultants are relatively rare,
That is probably true and itself is a huge problem if you decide to go this route.
Your SP Admin is partly at fault, from your post it sounds like your SQL Admin, Domain Admin, and network guys all need to get on boeard with making this work right.
I'm not sure what the SP Admin can do to improve Office. The built-in Sharepoint Office features suuuuuck.
If you are trying to use SP as it is intended there are very few cases where you would move several thousand files at once.
Unless you are collaborating with other people and part of that collaboration includes data collection. So now instead of one spot to keep everything, we have two. It's no big deal, but like I said when you avoid Sharepoint because of a shortcoming, you also lose it's benefits. In this case, we can't keep data, data collection scripts, or data analysis scripts in Sharepoint - they sit on a shared drive. Then we need ANOTHER version control system to be maintained in parallel with Sharepoint. Yay. Sharepoint is a Totally Awesome Place(c) for executives to post Powerpoints. My understanding is that Sharepoint is best left to setting up with NEW fileshares, since permissions and version problems hamper things on legacy network shares but maybe my admin is just overwhelmed.
When setup right the integration reallly is that good but the big bugaboo is training.
Again, the product is fundamentally broken on the client side if a change can appear to be saved, but in fact is not. How hard would it be for Excel to write the change and then read back the file for verification? I'm sure you are right that something is not set up just right - but man, how delicate can something be?
So if people aren't properly constructing their meta data ...
Reliance on metadata is a flawed concept IMHO. The humans (or at least some of them) will always do the bare minimum to make the annoying box go away. Even with the best of intentions, mistakes get made. Misspellings, selecting the wrong item in a dropdown, etc. Sharepoint search struggles mightily if the metadata isn't as expected. Even Windows search works better. And again, back to the shitty integration. If you don't click the boxes (missing metadata, edit this document, trust this document) in just the right order within Office, things go to hell and you end up working on a local copy.
Our local SP happily hosts .bat and .exe files without issue. Hell, the .bats launch right from the browser.
My admin isn't willing to open everything up. As a result I can't save files with "dangerous" extensions that might open automatically in the web browser. One big one is ".MAT" files for Matlab, which apparently also get used by Access as a shortcut. Another is ".JSL" which is a JMP script file. So our sharepoint Data folders are littered with text files that say stuff like "please go to \\someserver\datafolder to see the files for this project". Not Windows shortcuts, because God forbid MS supported their own technology in their "tightly integrated" product. And pretty Powerpoints, because that's what engineering needs is a place to stick and search for their Powerpoints.
Don't get me wrong, we had the same problem with our old Wiki. The problems that Sharepoint promises to solve are difficult and age-old (at least computer-age-old). But you can't really blame MS for overselling it, and that they most certainly do. I do not see our organization any better off for this experiment, and it is painful enough that I suspect it will go away the next time they are looking for money in the couch cushions... Sharepoint is quite expensive.