True, SPARQL does not allow "opening" transactions such that you can run one query, do some logic, and run another query while doing commit. Which was a pain for me. RDF4J has a non-standard API to do that, I think they are trying to upstream it to SPARQL 1.2.
> There's also the fact that a lot of triple stores are seriously half baked research-quality code if that.
Also true. Although excellent researchers who wrote one of the best reasoners (Pellet) decided to leave academia and make a production grade system. They succeeded with Stardog but you don't want to know how much a license costs.
> couldn't pitch any kind any kind of "boxes-and-lines" query tool [1] etc. that passed JSON documents/RDF graphs
I really enjoy this talk from one of the creators of OWL [1]. There, he makes a point that OWL is unpopular not because it's too complex but because it's not advanced enough to solve real problems people care about (read: ready to pay money for). I think the case you described involves VCs having clarity on how to make money off one thing but not the other. I do think that the Semantic Web 3.0 (if we count Linked Data as a Semantic Web 2.0 aka Semantic Web Lite attempt) will need a better (appealing to business) case than the one presented in the 2001 SciAm paper.