I have horrors about Indesign 5.5 no longer working, either due to the next Windows release, or just Adobe killing it off somehow. (Not cloud based, but it does phone home to their servers.)
I would dearly love to work in Scribus and Gimp instead of Photoshop Elements 9 and Indesign 5.5, but all my existing work is in the latter. Gimp imports PSD files, but it can't handle certain layers. I'm not sure whether Scribus would import a PDF and break it down into the original elements or not.
Fortunately, most of my covers consist of images (even the title font/author name), so they wouldn't be too hard to redo if I changed over. I can copy/paste the text.
I use Inkscape now for some vector stuff, like icons for my software, and it deserves a mention. Pretty easy to use, stable and very handy.
I guess the first step is to design a future cover in Scribus and see how it goes. The only reason I bought Indesign in the first place was due to Lightning Source and their steep compatibility requirements for PDF cover files.