I understand your point that Puntland needs to devolve power to her own regions, have one man/woman one vote, written constitution of her own..etc.
But you also are missing one very fundamental one. Federalism is either formed from ground up like USA or top down like Ethiopia or mixed one like Canada and India.
In Somalia it is mixed. Its top down for most of the country, but bottom up for Puntland. Since its top down for most of the country, then the constitution of Somalia is critical that it defines the relatonship between FG and FS. And also define FS and Zone, provinces or districts with in Federal states. Some states may have 2-3 clans there fore they may need some autonomy with in the state to elect their district government, to regulatae some activities.
Basically the Federal constirution is the key, nothing can be done and even the best attempt to do something will always bring conflicts. India and Ethiopian experience of constitution making may be useful as examples.
In the current circumstances its hard to say whether Mogadishu is abusing its power or puntland is asking too much. Whats too much, by what measure, by what scale. As Federal states get stronger will follow Puntland and then there is even bigger problem.
Many thought the whole issue between speaker and PM was the constitution, but does not look like it all now.