You can be the HoK or Nerevarine without using any magic, or by using only magic. You can be the Nerevarine by exclusively using throwing darts, or casting charm, fear, and paralysis on everything and never killing a living thing. You never have to intentionally ignore a quest reward in order to roleplay unless you are telling yourself your character is some kind of minimalist. You don't have to consider, encounter, use, or avoid using any particular form of combat one way or another and can be the champion. You have a special destiny in what you are to accomplish, but no special destiny in which tools you are "expected" to use to do this.
With the dragon powers, constantly having to ignore them is a constant reminder that you are playing a game that is designed to be played a different way than you want to roleplay. This is the fundamental problem with making powers specific to the player. It doesn't matter if its well implemented, or if you don't "have" to use it... these special powers are tied to the PC, forcing the PC to be a particular class. So you are then left with 2 options for the MQ... A Dragonborn that uses shouts, or a Dragonborn that doesn't use his shouts... either way, you still have to deal with this forced, alien mechanic, that is not integrated into the way the rest of the fantasy world engages in combat.
The fundamental problem I see with this is that TES is, as far as I am concerned, a ROLE PLAYING GAME. This kind of super-power backstory where you are told by the game's story elements and NPCs what type of abilities you should obtain to accomplish your goals instead of leaving you the hell alone to decide what weapons you want to study limits your ability to fully role play, moving it one step farther away from the pure role playing experience.
I get what you are saying, but if you do the amn quest then your character is embracing the fact that eh is dragonborn, ignore it and youll never learn shouts, and you wont have to use them.
Your right it limits RPGing, but the thing is that is who you are in the game.