As far as the network configuration is concerned, there may be a big difference: AJAX always communicates to a Web Server (either QVWS or IIS). Plugin acepts qvp:// pseudo URLs, so the communication is done directly between the QVS and the Client. This method is considerably faster, but requires ports 4747 and 4774 opened in both client and server both inbound and outbound.
When port 4747 is not accesible by the Plugin client, the server falls back to HTTP tunneling (port 80). This will degrade performance, because security packets are transferred and the network traffic and the use of bandwidth increases. Communication in this case is always between Client and WebServer on one side and WebServer and Server on the other.
I'd say that the biggest advantage of AJAX client is that it doesn't require any installation on the client's side, but it may require some design tuning.
It's up to you to choose one option or the other, avoiding tunneling when possible. In short, Plugin requires software installation client side, but rendering is WYSIWYG. AJAX doesn't need any installation other than a browser, but it may lack some design options.
Hope that helps.