In most cases transitions and animations would be messed up if back end conversion engine doesn't use MS office. Though MS doesn't recommend COM thing, yet there isn't any issue using it for conversions. Since using MS office would mean having windows machine along with office, cost shoots up. Best is to go for an open source based solution like Xembedo which can work on a Linux machine with free software. Though Xembedo provides high quality HTML conversions, yet PowerPoint elements like animations and media are not supported yet.
Still I like the idea of its simplicity, and the fact that its open source, but it is the current best option for a natively compiled program for Windows.