While there is at least one potential technical advantage to having subsites (using DNS for load distribution) and well-defined sub-communities have significant social advantages, subsites have significant question targeting issues.
Using tags, there would be fewer off-topic questions and “migration” would be a matter of retagging. Tags could be used to provide filtering by requested answer accessibility (newbie questions irritate some and excite others, expert questions are unintelligible to some and precious to others).
Tags might also be used for speculative degree filtering. (At Stack Exchange, some subsites tolerate or even encourage reasoned speculation [usually necessary for something like World Building but sometimes useful even for more mature technical topics] but some aggressively close speculative questions even when phrased in an answerable manner recognizing the need for speculation.) Other mechanisms for such filtering might be more appropriate.
Tag-related reputation could serve a similar role to subsite reputation and there would not be the issue of “association bonus” for those who have proven that they have basic good behavior.
It might even be possible/practical to have tag-set themes similar to sub-site themes with users providing themes and potentially even contracting artistic experts to design excellent themes for a favorite tag-set. Site “graduation” has been an issue at Stack Exchange; allowing a less popular topic to be supported as much as the users wanted might be better than centrally controlled specialization.
I do not know if such would be practical or even if it would be beneficial. This loose proposal might provide insight into a practical alternative or the subsite design might be the best option despite its weaknesses.
One of my areas of interest and (some) knowledge is computer architecture, which has some electrical engineering aspects, some software development aspects, some general less-mathematics-oriented computer science aspects. This mildly cross-disciplinary topic is somewhat fragmented on Stack Exchange (SuperUser has some questions, Electronics has some, Computer Science has some, StackOverflow has some [mostly technically off-topic]) and questions often enough get closed as off-topic with no migration. Other topic areas are probably even more cross disciplinary.