A bad main protagonist can easily ruin a game. Case in point: Final Fantasy Tactics.

However, it is worth noting that there is a difference between "bad" character and "not fully fleshed out" character. Just because a character is lacking in development or lacks moments of incredible depth, doesn't mean they're bad characters. Most people are actually pretty simple on a surface level, and without the proper circumstances arising, the depth they have will never show through.

Part of what ruins attempts at making a "super deep" character is creating utterly contrived situations that the characters are thrust into in order to show off their depth. Quiet, understated situations that highlight simple character design can work wonders at developing strong and realistic characters, even if they don't seem as "deep" or "fleshed out" as some others.