I've been working with the NPC Server so long, I can't remember how it is to use anything else
I suppose the main problem is in weapons. There are severe restrictions on what the client can do now, so they'd need to talk to the server to do anything like changing player strings etc. You'd also want to change some of the strings around to the new versions, such as clientr for example. Hmm... Also this.vars instead of server strings for NPCs where possible. Putnpc would be a small problem.
Other than that... Probably a great deal more things, actually. But I can't think of anything at this moment.