I am running into the same problem with my HTPC. I used Netflix for a long time but since 95% of everything I own (only a slight exaggeration) is from Amazon adding the Prime account was a no-brainer. Since Netflix was the only thing keeping me on WMC I'm going to switch my system to XBMC as much prefer its GUI over WMC (I know... skins and all that but who wants to mess with all that ).
I used WMC for Netflix for a long time and the app is horrible but it was the best option I had at the time. I haven't tried the Amazon Prime app on either XBMC or WMC but looking at what you're all saying it may be a moot point as those apps seem to have limited support.
My ultimate goal was to eliminate the need for any additional device (i.e. WDTV or Roku)... looks like I'll hold on to my Roku boxes for the time being
As far as having any kind of keyboard and mouse on hand as necessity? NO THANK YOU. I keep a logitech K400 close by in case something comes up where typing but that is definitely the exception and NOT the rule.
I'm sure you folks are aware of this blog but if you're not... http://assassinhtpcblog.com/
Again, may all be moot points if these plug-ins are no longer supported.. but worth investigating.