E.g. exporting private, closed etc. as boolean properties instead of optional empty-string properties.
Also in the response structure sitematrix.NN.code I think the NN key is arbitrary and unnecessary, so in formatversion=2 it could just be sitematrix.code
formatversion=2 can address T100459: SiteMatrix API has two fields called "code", which is confusing. See also T113034: RFC: Overhaul Interwiki map, unify with Sites and WikiMap.
@Spage: Those changes sound like they're well beyond what can sensibly be done with formatversion=2.
formatversion is about formatting the same data in a different way, not drastically altering the data structure. The latter is the same mistake Wikibase made that resulted in T95168: [Task] Remove calls to getIsRawMode() in Wikibase, and calls to setRawMode() in tests taking a long time.