1) I would like to have a uniform look between both my ML scenes and website. Is there any way to utilize the existing flash objects contained within the ML libraries in the web page?
No, no reuse today of your MainLobby scenes and Cinemar flash graphic libraries via the webserver. But, you can run a RDP or Logmein.com connection to a PC in your home running the Flash MainLobby3 Client application. For remote purposes, that aren't primary means to control one's house, this works very well and is secure.
2) Is it best to interface directly w/ Homeseer (events, scripts, state info, etc.) or interface directly w/ ML? HS is interfacing with all of my lights, cameras and thermostats so I am assuming that I should communicate directly with it. Can HS handle calls from a web page? Are there any advantages/disadvantages to this?
Since you have Homeseer and MainLobby, you have the flexibility to do either. If MainLobby Server has a plugin for a piece of hardware that HS doesn't then use what works. visa versa too. Some things (like a lighting controller) are best run in MainLobby3 Server for responsiveness to the touchscreens, especially Dim control using a graphical slider.
Follow the HTML examples. Expand on them as the technical hard work is now done.
4) I am assuming I will also need to utilize AJAX technology for accessing current state information (volume, light status, etc.). Anything I should take into account for this?
Follow the HTML examples. That's why they are there. There is AJAX examples (like the new iPhone scenes) and there is a non AJAX (the PPC example). If your display hardware supports AJAX, then go that path as it provides dynamic updates (no manual or timed refresh needed).