"Sequencing has gotten exponentially cheaper to the point that these types of projects are feasible (the paper you cite is actually a proof of concept for their metagenomics pipeline), that everyone is just sequencing this shit out of everything. "
Well that's exactly why I'm excited, but your phrasing makes it seem as if this is just a matter of course. Game changers in many fields often arise because some previously expensive resource becomes economically more accessible (cheaper). You make it sound like "The Model T Ford is just a low-hanging fruit of cheaper gasoline." Nothing is exciting if you pull that angle.
Regarding (1): Yes, and that "lack" is why I currently have a job (employed as a computer scientist helping analyze big data). If nothing was "lacking", analysis would be as easy as a biologist pushing a few buttons in a spreadsheet-like program, and nobody would need a computer scientist helping them.
Regarding (2): That's only a technical issue that is the main contributor to (1) -- were it not for short reads, analytics would be much easier.
Regarding (3): From some reports (can't confirm right now but can look for a citation if you're interested), I have seen exactly the opposite -- that the estimates of biological variation from metagenomic data are actually skewed towards higher diversity than expected. Could be due to errors in the pipeline, and is being worked on, but some of that variation could also be explaining legitimate biodiversity.