So then what you are looking for is examples of how it is effecting the game as a whole. more specifically how it is effecting Fontan and its politics and game play?
Basically, yes. There is no debate about economic or military efficiency, as Tom has stated. Those issues are "givens" for this case. The debate is if clans are inhibiting gameplay.
Regarding the cases you mentioned, I have a question: so a person was elected without debate over a person who put in some public/private effort. Can you think of no other reason that person was favored? Any differences in military service, time in realm, or whatever? I'm not saying I disbelieve you or not; just trying to get clarity on what you are stating.
Regarding the general's use of the military council and orders; are you saying that some nobles are receiving orders that other nobles (presumably in the same armies?) are not? And, furthermore, how are you claiming those orders are passed? Are they going IC, OOC, or what?
Because conflicts between generals, marshals, sponsors, and judges are normal and interesting. What you need to demonstrate is that this isn't an RP conflict between IG political powers, but is primarily a conflict stemming from an OOC clan attempting to force other players to play its way, or to exclude other players from its turf, or some similar harm.
