They were almost all avoidable with a bit more planning early on. If you look at the questions here on GBA, a fair proportion of them involve people who have dug themselves a hole by not thinking through the implications of their designs on their insulation strategy, roofing materials, or other facets of the construction. Redirecting water from one area of the roof to another can be a challenge, properly planning your crickets, gutters, and downspouts to make sure that your house is dry and away from rotting or molds is another challenge as well. My advice to people who want to design their own house, or draw their own construction drawings, is to run the results past someone with design and construction experience, so these types of things are addressed way before the framing starts. Roof crickets are an integral design to almost every architectural design and should not be left out. Like anything else, in general the more you do it the better the results. Experience helps you build a skillset of things that work, and those that cause problems - like bump outs on two floors sharing an exterior wall - and avoiding them. You go back and forth between the plans and their implications on the sections and elevations.

Architecture, like the design of most objects (computers, furniture, cups, cars), is a three dimensional iterative process.