Silent Assassin addressed many of the criticisms concerning the gameplay of the original game: The control scheme has been streamlined to better mirror that of a standard shooter: an optional first-person perspective was added, and a visual meter was added to give the player the ability to gauge enemies' suspicion level for stealth purposes. While the "suspicion meter" generally reacts appropriately (such as when the player enters a restricted area or draws a weapon in public), there were some sensitivity issues, possibly bug-related, which caused enemies to react adversely to the player for seemingly innocuous actions, such as running indoors or close proximity. This feature was improved upon in the subsequent games of the series.
Also introduced in the game was the concept of a post-mission ranking system, in which the player is given a status based on how they completed the mission, rated along a stealthy-aggressive axis, between "Mass Murderer", a non-stealthy player who kills everyone, and "Silent Assassin", a stealthy player who manages to complete the level without being noticed and only killing the intended target(s). The game rewards the player for critical thinking and problem solving, encouraging the player not to treat the game as a simple shooter. Achieving a Silent Assassin status for a mission rewards the player with bonus weapons on some levels.