Me, as a DM: Another rapier, how original. (eyeroll) Let me guess, high dexterity and a two-level dip of spellcaster, too?
Me, as a player: Yeah so my next character has a high dex and a two-level dip of spellcaster, so I'm going with the rapier...
I'm not sure how that can be fixed; people are gonna always gravitate to it because (1) it has the best damage of any Finesse weapon, and (2) Dexterity is the most important stat in the game. Any proposed "fix" to the rapier is going to involve changing (1) or (2), and your players will never go for either.