The current way is great, but it requires importing API files which makes it, in my opinion at least, unnecessarily complicated.

I think a simple way to set the value using simply IMC messages should be allowed
something like sending an NBT compound with a stack (or string for or dict), an integer value and perhaps a boolean to determine is it's a pre or post assignment.

I think it would make it a lot simpler and would be an incentive for other mods to add compatibility with EE3.
If you don't feel like implementing it but liked the idea, let me know and I can submit a PR myself.

(I talk as a mod author who added EMC values to all the items in his mod but would love to use a simpler way that doesn't require any use of APIs)

We could do that, sure. I want to keep the Json based methods too though. The API package is not necessary - it just gives folks a structure to mimic with their own, or just tell them how to structure the Json strings to send to EE3.

Plus, since it was originally written, EmcValues for items are all Corporeal now so that simplifies things QUITE a bit :)