1. Lack of definition files for some isomorphic flux implementations ( like yahoo/fluxible ) ;
2. Lack of big projects written with TSX to learn from ;
3. No support in WebStorm ( even 11 EAP, dated 09.09.2015 ) for TSX files ;
With No. 1. as most annoying I would recommend for anyone trying to do isomorphic NodeJS + TypeScript app to be really patient and to expect writing commits to DefinitelyType repo.
Kudos for TypeScript team for implementing TSX it would be great when it's out of beta.