HL7-all-the-things as a solution to interoperability (hey, v3 is this new fancy thing called XML!) The incentives are often backwards for hospitals to want true interoperability - this is with HIEs have been known to fail - "Why should I give my competitors all of these leads - I mean, patient data?". Add on top of that HIPAA (and state-by-state) requirements, and you impose significant overhead to sharing data even if an organization wanted to.

Health IT is a difficult problem not (primarily) because of technical challenges but because of human challenges (arbitrary updates because of regulatory requirements, requirements in software to mirror what was done on paper years ago, etc.) None of the low-hanging fruit will really change with HIT until we make incentives line up with what's best for patients (which will probably mean changing a lot more with the healthcare industry as a whole).