What does it matter if it's one app or two?
1) Turf wars. Facebook suddenly has two app icons on your launcher and twice the application storage thus blocking other potential comms systems, like Line/Telegram/etc.
2) Personally I want all my facebook stuff in one place. I only use Facebook private messaging very occasionally and only for email-style comms, not chatting (I don't really do online chatting). I would also like Lync folded into Outlook (the conversation history goes there anyway and Outlook can show presence just the same as Lync, so I'm not sure why they don't just make Lync an Outlook extension - I can't think of many MS customers who would be buying Lync without Outlook).