Uh, you're right, exporting everything as different MDL files and morphing the models to play different animations is definitely not the way to go

But I think you misunderstand what I'm asking for. I'm looking for a way to keep my animations separate in Maya, but merge them into one MDL file after exporting.
> Why do you think this is a limitation?
Where do I start?

The pipelines I'm used to working with treat animations and models as independent. I.e. you can export animations one by one and in the engine you decide which model you want to play them on.
This is pretty convenient since the animators can work independently from each other and export at different times. You can test and troubleshoot animations separately from each other and you don't run the risk of introducing bugs in one animation when you're fixing a different one.
Maya files with a lot of animations in them are unwieldy and hard to edit, especially if you want to change timing (if you lengthen or shorten an animation)
Also if you make a change to just one animation, you have to redo all of the markup work for all animations in MED again. And again. And again. It gets old pretty fast, and it's error prone.
If you are working with a team of animators you have to come up with a procedure to merge all of their work into one master Maya file. These kinds of things are usually tricky and error-ridden, and IMHO this is an unnecessary source of aggravation.
I could go on, but I hope I've made my point. It's just not a very good pipeline, especially if you have a lot of animations and several animators working on a project.