The philosophy is to keep the modules as simple as possible, so they are easy to understand but can work together to do something powerful. Some modules like the wavetable oscillator and granular are a bit more advanced than the other ones.
Related to this, there has been a lot of debate about the Sampler module in other threads, some users like @tiger001 and @IvanS want the sampler to have multiple slots because they need to use it for percussion samples while people like @Mercurial and @BrettSaberhagen have a different use case and maybe prefer the sampler to just have one slot.
I think it would be better if the sampler just has one slot, which makes it easier to understand it and so there is no confusion about parameters of the sampler applying to all of the slots simultaneously, but then there is more work to be done in the patcher grid to build a typical drum sample setup and perhaps the sampler also becomes creatively less interesting by itself.
In the case of the tuner/scope here the functionality is fine where it sits right now, in the MIDI module, because you use the MIDI module with your external oscillators for example, and then you want to tune those, so it makes sense to feed their signal back into the MIDI module. But, there is also a pro to having it in the input module instead. I don’t think it’s necessary to make it into a seperate module.
The modules are automatically scheduled on the 4 processor cores of the SSP so generally you don’t have to think about that too much.