Only co-op is a disappointment.
Story is the same in both versions. You as Sam Fisher help a terrorist to escape from prison and that way you get to be among them as a double agent, because at the same time you are also working for the Third Echelon. On the course of the campaign you can choose between 2 or more options on how to progress. The choices you make can have severe consequences.
Graphics are of course better in Xbox360 and they are almost all daytime missions, when in Xbox version all missions are regular nighttime affairs as in previous Splinter Cell games have been. Graphics and environments are not quite as detailed as you might expect to see, but they still look good. Sound includes more weather and other environmental effects and the bulk of the game is to carefully listen what happens around you. Music fits the mood perfectly, but it is not particularly memorable either.
Gameplay is very different from Xbox version mainly because as I already mentioned they are mostly daytime missions. Choices you need to make are often showed as a separate interactive cutscene and not among the actual gameplay as it was in Xbox. Controls on the other hand are identical between the 2 versions. The differences between mission structure induces a feeling that in order to experience Splinter Cell: Double Agent as its fullest you need to play both Xbox and Xbox360 versions. This feeling is correct.
Multiplayer is a big disappointment especially in co-op missions. In Chaos Theory you played as 2 younger Splinter Cells in the same locations as Sam Fisher, but now co-op missions are just a variation of the regular multiplayer modes. I expected that same great true co-op mission quality, but it never happened.
Normal multiplayer is 3 agents vs. 3 mercenaries and the agents are trying to download data from computers when mercenaries are trying to stop their intentions. Mercenaries are controlled like a regular first person shooter and agents are controlled like Sam Fisher in the single player campaign. It can be fun, but in my opinion it requires a somewhat coordinated team to really enjoy it.
I recommend Splinter Cell: Double Agent for Xbox360 to all Splinter Cell and stealth game fans in general. Just do not expect to see that same quality in co-op missions as you might remember from Chaos Theory.