You should be able to change the format that we use to create the HTML tag for videos.
Open up this file in a text editor:
C:\Users\[USERNAME]\AppData\Local\Windows Live Writer\ResourceCache\live\VideoProvidersB2.xml
Search for the video service you use and just edit the embedFormat and editorFormat nodes. Feel free to email us if you have a problem:
wlw-team@microsoft.com
-Brandon Turner [MSFT]