This is by far the best method I've found. I use TextMarker Go
. It's simple, allows you to select text than Right Click > Mark this Selection to mark it. It doesn't save your highlights, but I don't care (as I'm clipping them). There's some add-ons that do, but they're not as simple and don't work with current versions of Firefox.You can set up to three different color options (just go to Firefox > Add-ons > TextMarker Go Options). A regular click on "Mark this Selection" will get you the first color, Ctrl + Click the second, Shift + Click the third.
Then select what you want clipped and send it to Evernote with the Web Clipper (which allows for online AND offline clipping). Unfortunately simplifying the formatting doesn't work but you can change the font and size and the highlighting usually looks find (adjusts it's size, etc) unlike with some other methods. Also some text might simplify itself as you see in the second picture if you clip from a selection (not if you clip from article view or fullpage). Copying it to a note by hand will simplify even more formatting (like the word "Wikipedia").
The downside to this method is that it leaves some spaces highlighted sometimes between changes in formatting (links, underlines, etc). You can fix these by backspacing the blank space than adding a normal space. It's tedious though so... you might want to get used to the spaces. Most sites aren't as formatted as wikipedia, so it might not bother you anyways. Pictures:
Article View | Selection Clipped | Selection Copied by Hand | Original Text on Wikipedia (well not quite so original as I have a few add-ons for it), but you can see the lack of blank spaces.