Sadly for me, I am a creative sort who can come up with great ideas for mods but I lack the technical expertise to execute everything I'd like to. I have no idea how to make this idea work in game, but if someone else likes it and has the skills I lack, well, at least I put the idea out there.
For anyone familiar with MEHEM, its obvious that Shep survives - but I think he/she should be scarred. I am working on a mod to progressively age Shep from me1 to me3: more wrinkles, grey hairs from the stress of being Shepard and having trillions of lives in your hands. I also think it would be a good idea to keep the bloodied, bruised face texture from the endgame in MEHEM - to show how worn down shepard is, or at the very least, those injuries would take time to heal. I dislike how Shepard looks the same at the end of Me3 - after that horror and stress - as he or she does at the beginning. If Shep is going to survive - like in MEHEM - he or she should be scarred, bloodied, and bruised by the battle. It just seems so thematically jarring for Shep to survive unscathed, especially as Paragon, considering that that alignment feels the weight of all the lives at stake much more than Renegade.
This is both an idea and a modding how-to question. It applies mostly to textures, so I'm going to move it to the texture area.
From your description, the MEHEM aspect is a bit ancillary. You seem to want to convey aging across the trilogy. How Shepard appears for the final minute or so in game during the Memorial Scene is minor to how they would be appearing for the other 150 or 200 hours of the trilogy. Not to mention during that scene Shepard's face IS already bruised and bloodied, as you describe.
A few other thoughts:
--Scars from ME1 can already be carried into ME2 and ME3 with mods. You could certainly make some new textures that contain more significant scarring.
--Most folks wash dried blood off their faces, so having Shep walk around everywhere with a bloody face isn't necessarily realistic.
--I think the game conveys relatively well that medigel is a miracle substance that works very fast at healing wounds. This is the excuse/reason BW needs to not have everyone walking around with fresh cuts.
--Facial bruising could add some realism, however, I think the idea is also that Shepard doesn't bruise easily due to the cybernetics. This is the same reason the scars weren't continued from ME1 into ME2, since Shep was rebuilt. However, unless you went to great trouble, the bruising would have to be in place in game all the time. That then constantly shows injury, but no progression of healing, which also seems immersion-breaking.
--I think showing an increase in gray hair is a great idea (not sure how the cybernetics would affect that), but it will be very difficult if not impossible to pull off due to how the hair coloring system works in the games. ME3 is the most flexible, since it has actual stranding and real highlights. You have no control over the location of those highlights, however. So, gray highlights might end up looking good... or not. Also, you'd have to either gibb them in, or alter the CC itself to make the new colorations selectable.
--Putting more wrinkles into each of the face textures for ME2/ME3 would be easy. You'd have to be very careful which files you incorporate them into, however, or they will affect characters other than Shepard.