The "undercover missions" were annoying and they broke up what would otherwise have been another good game.
Other than that, I liked it. It was more of the gameplay that I have come to expect from a Splinter Cell game, with the addition of the complications of trying to keep both sides happy with you... there were timed decisions where you had to decide which team to play for (whether to kill somebody, etc.). This was a nice new twist on what has become familiar, something to spice things up a little bit in the series.
Anyways, the game is worth playing through at least once, but honestly, I would recommend using some sort of game guide, at least for the "intermission" stuff, so you can get through it a little faster and get back to the real game.