The modular ports is probably a good idea, but I also find the chosen module size a bit of a uncomfortable middle ground.
On the one hand, they're too small for some very obvious standard ports you might want on a laptop, like for example an RJ45 port. Or multiple/vertical USB-A ports. And they're too small by a relatively small amount, so if the laptop had aimed more at Thinkpad T size thickness (still not terribly thick) rather than Macbook Air thickness, the modules would have been much more flexible (and maybe we could have had even better keyboard options).
A really significantly sized bay would have been quite interesting too - old T-series used to allow you to add a second battery, a big bay could have allowed breakouts for sensors, fpga add ons, etc. Perhaps allowing a double-wide might have been a good way of addressing both.
On the other hand, the modules are still pretty chunky. You don't want to be using one out of its slot, I don't know what sacrifices were made in terms of space in order to have what in many peoples laptops are going to be pass throughs, but the Framework has a relatively disappointing battery, so perhaps that's an effect of the reserved space.