The thing that has advanced the most is the scripting of the game world - it's clear that the familiarity of the engine and the development tools has helped here, and Episode Two feels much less artificial in the scripting of the actions triggered by your progress. It just flows smoother while a level is in progress. The addition of physics to scripted events also creates some truly impressive sequences.
Some rough spots remain, and the long loading pauses between sections are bit annoying, but I guess it can't be helped - the engine just isn't set up for constant streaming of content. Puzzles, while fairly rare and sometimes optional, are also exceptionally well done - not immediately obvious, yet not so hard as you'd have to alt-tab for a solution off a spoiler site to proceed.
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