CofD's Skill set is the way it is for the same reason their Resource Merit works the way it works: the character sheet is an abstraction and meant to work within the context of a table, with a consistent storyteller that will look a master photographer who wants to suddenly write a Nebula-winning novel a look like 'yeah, okay, settle down, Renaissance Man'.
If your dude with Academics five is a historian, he probably shouldn't automatically know all about Law. However--he does have a 5 in Academics, which speaks to a level of dedication within an academic lifestyle that might, with some time (i.e. research) give him the knowledge needed. So someone with Academics 5 might be able to roll at a low difficulty (no penalties) to answer an obscure history question, but if the question is about Mississippi Law, he might be like, 'I can totally answer that if you give me a few hours and an internet connection'.
The problem is people don't viedw it this way.
Crafts is a weird Skill, no doubt. However, the things that fit into Crafts are often not terribly useful within a campaign as the game was designed to be played. You typically use Crafts for mechanics, of making explosions, or building traps, or eventually, making weapons. These are things that people in the situations the characters find themselves often need to learn to do as a group of Skills.
One good way of viewing Crafts is probably the same way Drive views riding motorcycles. If you're not familiar or forgot, if you have no Drive Skill, you can't ride a motorcycle at all, or at least with a lot of difficulty, mostly because you don't have the Skill (-1), and you don't have the Specialty (-2, see next point). If you have Drive, you ride a motorcycle with a -2 penalty. The only way to get rid of this penalty is by buying the Motorcyle Specialty for Drive, which works as a normal Specialty, and also gets rid of the Penalty (which is why if you don't have the Skill at all, you're at -3).
It would be easy to apply this backwards to Crafts and Expression and Academics, for example. When you take your first dot in the Skill, pick an area. Anything that falls into any other area gets a -2, unless you buy the appropriate Specialty. Of course, this comes with its own problem, because let's say my character has Academics 5 and he's a Historian. Okay, great. But he's tired of taking the -2 to Law. so he buys the Law Specialty. Now he has 5 Skill dice for History stuff, and 6 for Law stuff. WTF?
So, you know. Somewhere in between.
Personally, I'm fine with how it is. PCs should be special in some ways, and making people who have (often criminally underused) Skills like Expression, Academics, Science, and Crafts effective polyglots in those areas is fine.
Plus, while the CofD is gritty and all that, it's still pretty shiny in terms of character tropes. How many scientists on TV and in movies are surprise experts in basically every scientific field? It's almost like it should be a trope of some sort.