Oops sorry it took me awhile to reply I was away. Yep Nathaniel and Jonas look very similar and share the same voice acting on purpose. It's not revealed in the main story yet why this is, but it's hinted in this game that Nathaniel is starting to awaken.
I always thought language barriers in these kinds of stories would be interesting to explore but I think the trouble is in how much it would interfere with pacing and my lack of knowledge in linguistics. Probably bridging this gap would be an arduous process, and Isaac would probably lose his patience and go off sulking for periods of time but eventually I think maybe even a tighter bond could be formed.