I don't think upgrades are needed as such, because they are always forgotten (as already stated) as soon as they are given to the villains anyways. I think Marvel really needs to start making new villains, because with Civil War and their attempt to make most villains almost "anti-hero"-ish there is quite a lack of actual villains.
The ones that are still around are a bit tired and repetitive, for example Magento has been raped to death to be honest with the Xorn thing etc. So they really need to get out there and start creating more antagonists for their stories, a writer who is very good at this is Dan Slott (which is why I'm DEFINETLY picking up Avengers: The Intiative). Many writers lack either the knowledge of continuity or just the effort of picking up some of the many villains that Marvel let slide into obscurity.
My 2 cents, probably worth ahellavalot less though.