I would go as far as saying make a standalone version with a Zepto-lite, then add an IE8 shim of some kind (like this and maybe others, like an Array.prototype.indexOf). When IE8 dies, just remove the shim and no further work required.
For the other libraries, I would say "drop 'em", but others have shown interest in keeping them. In which case, I'd say that @daff has the best idea of formalizing Universal.js