When you move your controls you are changing the profile of your wing at the location of the controls. By deflecting the control you change the amount of curvature of the profile. Larger control size means that you get a greater change in the curvature of the profile for a given control deflection. (Basically you are using two different approaches to do the same thing.) This change in profile has the effect of changing the amount of lift that section of wing is trying to produce.
The problem with increasing the curvature of the wing (by either extra control deflection or increased control size) is that you run the risk of asking too much lift from that section of the wing, causing it to stall. This is the phenomenom (sp?) that leads to aileron "reversal" at low speeds. In addition, the change in controls leads to changes in the wing properties which are related to flutter (a problem related to wing elasticity and aerodynamic effects). Flutter usually results in sudden departure of wings from airframes and begins so quickly that there is usually little chance for the pilot to react. The weight and balancing of the controls is also effected which has bearing on flutter and also control forces that the pilot has to deal with.
Also, when you work the wing too hard by increasing the aileron deflections you run the risk of stalling the wing at higher speeds than normal and overloading the wing at speeds which are below the max maneuver speeds. Both of these things are not good.
In reality the design of control surfaces is a very complex task and is an artform on performance aircraft. Many aircraft were lost trying to perfect it.
My advice to anyone is not to stuff around with the rigging or sizes of control surfaces on a plane if anyone is going to put their butt in it. It isn't something to be done lightly, I've already seen the aftermath of an accident where someone changed the skins on a glider's ailerons from fabric to aluminium. This changed the weight and balance of the aileron and caused flutter which took both wingtips (and most of the rest of each wing) off. Not pretty. Fortunately (in a way) it was the owner/pilot who had made the change and was flying at the time, no one else was killed (natural selection?).
WRT changing the throw range of a control: this also increases the drag that you get when you make a control input. More deflection = greater drag.
Manufacturer's put limits on things for a reason. If you want to exceed them, seek expert help...
btw sorry for the wall of text. I hope it's informative.
