What's the difference between the ASP.NET Master Page, and the MVC Master Page? And the AJAX Master Page for that matter?
Mostly it comes down to the default controls and inheritance.
The AJAX Master and ASP.NET Master both inherit from System.Web.UI.MasterPage, while the MVC Master inherits from ViewMasterPage.
Obviously, these give you slightly different controls on this - as stated by John Clayton, the ViewMasterPage exposes the Ajax/Html/Url helpers and the like, which are not available to the other MasterPages.
Other than that, the default controls are slightly different:
The "lifecycle differences" come from the Page/ViewPage, rather than the MasterPage/ViewMasterPage controls.