Agreed, but it's true we don't know the OP's requirements and what exactly his unit is supposed to do.
Assuming they take care of the requirements properly, the question of which approach would be more "reusable" is interesting but hard to answer in a very general way.
First, you need to exactly define (of have your customer define) what reusable means in this context. Should your design be usable in other contexts? Should it be easy to modify if extra features are needed? Should the customer be able to do this on their own once you've delivered the project? What amount of documentation are you ready to produce and give away?
Does reusable here mean longevity? So should your selection of components ensure that they will be available long-term? If so, how many years from now (minimum)? Does that alternatively mean that your design should be easy to port to different parts (especially the "CPU")? Does that mean that this porting would have to be minimal AND doable by the customer years from now and without your help?
Selecting a soft core on FPGA rather than a MCU is a tough choice to make for achieving the above goal. A soft core-solution may look like it's better because you have control over the processor itself instead of being tied to a specific vendor, but it looks that way on the surface only. In many cases, a real-life implementation of a soft core on some FPGA will require specific resources of the FPGA you select and thus the porting effort to another FPGA down the line may not be as easy as it seems. Then there's the question of the architecture of the soft core itself. If you're going for a vendor-provided soft core with an odd ISA, you're tying yourself to this vendor. OK some vendor soft cores are open and you can reuse them on other FPGAs (but that may take effort), some are not... Then you need to consider if an odd architecture will not make your design actually more difficult to reuse than using an off-the-shelf MCU with a well-known and well supported architecture.
Then you need to consider validation. I don't know what your customer expects, but in avionics, regulations are stringent. You need to follow strict standards. Validating avionics software is hard as it is, but if you have to validate a soft core on top of that (including its particular implementation on the particular FPGA you select), that's a lot of work.
Again I don't know all your constraints, but if you're using a MCU with a pretty standard architecture (say ARM), write decently portable code, properly isolate all the hardware-related code (drivers, etc), and/or use a well-known and well supported RTOS, this should be straightforward to port to a different MCU later on if the need should arise.
A lot of considerations, but choosing a soft core, even though it may look like you have full control over every part of your design, is not necessarily the wisest choice here. And with all that said, you should definitely consider discussing that with your customer in details, exposing the pros and cons of various approaches, taking the regulatory aspects into account, and let them decide based on your technical inputs. Just my 2 cents.