Guacamole has much better performance. Your browser and the guacamole server communicate using a custom, better-performing protocol (http://guac-dev.org/doc/gug/protocol-reference.html). While guacamole can still connect to your server with VNC, it also supports RDP, which is also faster. Even when using Guacamole as a proxy for VNC if your guacd and VNC servers are on LAN together, because the guacamole protocol works much better over high latency connections than VNC does.
Edit: also, Guacamole doesn't use Websockets, which makes it much easier to proxy with your standard HTTP proxy software like apache, which didn't get a Websockets proxy module until 2.4 (Ubuntu 12.04 is 2.2).