It has some significant changes as well as several minor ones such as moving away traditional Terrorist versus Counter-Terrorist scenario and incorporating a matchmaking and Elo-derived rating system to help keep players and teams on even footing. Most notably, the game uses anime models to market it in Japan.
The weapons from Counter-Strike: Source make a full return.
Along with NEO, there are several Flash videos made by developer Romancework, titled White Memories. The Flash novels have a continuing storyline and even some portions of gameplay that loosely resemble Counter-Strike itself.