I know this post is a bit old but I found it while searching with the same problem. There are various potential solutions that I have eventually discovered. Direct import of an html file (via the import folder in windows Evernote) only works for simple files and normally fails to include pictures and also changes the formatting. In my experience this is actually more likely to fail if you embed pictures etc in the file.
My best solution is as follows: Save the html file to dropbox. Open the file on the dropbox web interface - you need to open in a new tab in order to see it without any dropbox clutter. You can then use the webclipper.
Another solution that works is to cut and paste the file from chrome into gmail and then either use the webclipper from there or even better, if you are a premium user, e-mail into Evernote