The message format for the JSON, BSON, and XML serializers should interoperate between MT 2.x and MT 3.x, I purposefully didn't touch them to avoid breaking changes that require a fork lift upgrade of the entire system at once. Versions should interoperate both directions without any issues. In fact, I should build a sample to demonstrate that it does indeed work as expected.
The encrypted serializer in 2.x (based on an older encryption format) has been replaced with full AES encryption in MT 3, but if you aren't using that then you're fine.