Why do EMR systems come with ICD-9-CM codes installed instead of SNOMED CT? It may very well be that it's because that's what providers get paid for. It used to be common wisdom that biggest reason for installing an EHR was to improve upon payment. With meaningful use, the focus is shifting from that to exchange of clinical data.
If you look at the ACO rules, the shift is also towards exchanging clinical data.
If you look at some of the work happening in Health Information Exchanges that payers are setting up, there also is a move towards clinical data exchange.
If you look at the recent work of the HIT Standards committee, you see the focus on quality measures has shifted to clinical vocabularies.
I welcome this shift, and see it as the start of a Healthcare Revolution.
This sort of revolution won't be without its challenges. We definitely need established mappings from ICD-9-CM and ICD-10-CM to SNOMED CT to support them. As HIMSS mentions in their post, it could take some time to implement.