In my opinion, there are several mechnical issues before and during the operation of fuel cells.
It starts with the MEA manufacturing for example mechanical affects caused by heat and hot pressing and continues with the assembly of fuel cells and the applied compression force.
Getting a fuel cell into operation causes hetup and therefore temperature elongation of components.
Water production during operation causes membrane swelling etc. Higher or less load causes changes in water production which results in swelling and shrinking of the mebrane, ....
This is just a first rather brief glimpse into your question.What are you aiming at with your question?
Aimen, your question was similar to what i asked (to myself) 6 years back. i am from mechanical eng background but wanted to be in PEM fuel cell r&d. So, the most obvious choice was improving the cooling methods of PEM fuel cell (thermal management). It can be done experimentally or using CFD. I started with air cooling, now i'm into liquid cooling. there are still tons of work that can be done in this area as improvements in cooling capability would lead to more compact (smaller) stacks.
CFD can also be applied for flow channel designs for hydrogen and air both. but it needs to be simulated under reacting conditions, meaning you should have a fuel cell module with your CFD. For thermal engineering analysis, it can be done based on non-reacting environment. New concepts for flow channels can be researched, one of the newest is based on design-by-nature.
It must also be noted that the control algorithms of a PEMFC can also be a mechanical issue.
If you're into manufacturing process, then r&d on cost-effective and highly autonomous stack assembly would be one aspect to be looked into.