Theoretically those two problems can be solved concurrently, but still-- favicons, hotkeys, and the ability to drag and drop solves most of my problems with tab organization. I use alternate windows only when really necessary.
What I'd really like is to have a second, isolated firefox process that I can run alongside my main one with as much functional independence as possible. One process will be for the relatively safe, familiar, and stable, text-oriented type sites with minimal advertising (hacker news, gmail, wikipedia, python.org, clojure.org, paulgraham.com, etc.), and the other process will be for heavy sites, new/risky sites, or otherwise problematic sites (eg if I have a youtube tab open I can't ctrl-PgDwn past it, when I hit that tab I have to stop and use the mouse-- a pain in the ass).
While Chrome's process-per-tab model is really nice, they're still all tied together and there's a risk of losing everything sometimes.