I just got the game and played it for the first time.

There is one thing that bugged me a bit.

The fact that all houses can muster the same amount of pieces (knight, SE, footman, ship)

I think it would have been a bit more interesting if it would have been different between each house.

Say:

Greyjoy having more ships units to muster.

Starks having more Knights.

…

I'm not sure about the balance between the houses with the unit but I'm sure better men than me can think of the right balance and making it more fun that way.

 I think it's pretty good right now, for instance, when the muster troops card is drawn then the player(s) with the most stronghold/castles can muster more troops.  Additionally only the player(s) high enough in the king's court can muster on a regular basis.  If you mean, however, that in order to show the diversity between the houses that they should be able to muster differently than I have no solution for you, but feel this would greatly unbalance the game (more so than it is).  The diversity of the houses is represented by their starting set up (between the units, castles, supply and influence tracks).

My two cents.

 I also want to know

To house rule this would be a complete nightmare, AND you'd likely need more troop types.  However, it's not a terrible idea.  The Lanisters having another knight or two, but less ships, for example.  Greyjoy having more ships but no seige engines.  Whatever.

Had it been in from the start, it could have been used to address the (perceived) balance issues too, but it also adds more colour to each house imo.