OK, here's my take on some rules that should (IMO) be added to the book:
Most martial adepts have a list of what are known as "alternate disciplines". The typical example of a given adept does not have access to any of these disciplines, but specific members of the class may have knowledge of the discipline in one of two ways.
The first is to have neglected training in one of that class's ordinary disciplines. Any martial adept may choose to start play having no access to one or more disciplines that the class normally has access to, having been replaced by the same number of disciplines from the alternative list.
Any character who takes an alternative discipline for a class that does not have the discipline's associated skill as a class skill, loses as a class skill the skill associated with the neglected discipline, and gains the alternate discipline's associated skill.
The character may also trade proficiencies in weapons associated with the neglected discipline in favor of those associated with the alternate discipline. They can only gain proficiency in an exotic weapon associated with the alternate discipline if they lose proficiency in an exotic weapon associated with the neglected discipline, only gain proficiency in a martial weapon associated with the alternate discipline by losing proficiency in an exotic or martial weapon associated with the neglected discipline, etc., and in all cases can only gain as many proficiencies as they lose. They cannot lose proficiency in any weapon that is associated with both disciplines. They may trade in as many or as few weapon proficiencies as they like.
The other way to gain access to an alternate discipline is to train with a master of the discipline. A master is defined as one who can initiate 5th level maneuvers from that discipline. Training requires one month and the expenditure of 1,000 XP. When training is complete, the martial adept may add the discipline to the list of disciplines from which maneuvers may be learned with levels in any class that has the discipline as an alternate discipline, and may further replace any number of maneuvers already known from any class that has the discipline as an alternate discipline with maneuvers from the new discipline. Unlike the normal method of replacing maneuvers, however, any maneuvers lost must be replaced with maneuvers of a level no higher than the lost maneuver.
The martial adept also adds the skill associated with the discipline to the class list of any classes that have the discipline as an alternate discipline. The adept does not, however, gain proficiency in any additional weapons.
This should make it easier to write classes, since you can just say "these are the alternate disciplines", rather than explaining the rules behind them every time.
This assumes we're using The_Demented_One's system; I happen to like it best, but that doesn't necessarily mean anything, heh.
Oh, and I forgot to mention before: your link to Untamed Essence is wrong; it links to Krimm's alternate Desert Wind disciplines. That, and Way of the Gear does not indicate what its associated skill is.
And I updated the table with the Far Realm discipline (linked to by SurlySeraph earlier, I think you missed it) and the Bladed Thoughts and Placid Lake disciplines (linked to by me earlier). That brings our author count up to 18. It also means we are currently at a cool 50 disciplines.