I've only played it twice, but there are pretty extensive changes. -Attributes are significantly different.
-Character creation is now a point buy system.
-A drama point style mechanic has been added, and combat pools were consolidated even more.
-Several setting and stylistic changes have been made, including the addition of what were Otaku now called Technomancers, wireless Matrix, hackers instead of deckers, corporate changes, some new tech upgrades, etc.