From my understanding Raphael is specific to the SVG context. Two.js is renderer agnostic, you can choose whether it draws in SVG, canvas, or webgl. This is one of many differences between the two.
Rapahel does SVG but most importantly it also renders VML when SVG is not supported by the browser, as a result it supports IE6+ unlike two. (don't get me wrong I still think two is great)
Not the same - e.g. rotating a set of elements causes each individual element to rotate around their individual centers, rather than causing the group to rotate around a central pivot.