It really is awesome and you should play it if you didn't already. It's on par with what Valve made themselves - especially the second and third parts. 

 

Most of them are fairly subtle.

The biggest changes that I noticed were the new music that has been added to a few sections, new special effects and sounds in a lot of places also.

There is also a large compatibility update to the mod as the original Minerva got somewhat broken by an Episode 1 patch that valve released at some point, which made the mod unstable and introduced a few visual errors in things like the waves on the beaches and other areas, these are all fixed now.

There's probably more stuff, but that is what I noticed on my play through. 

here is a link to the changes - https://hylobatidae.org/minerva/blogsheep.php?action=articleinfo&id=118 .
Valve actually hired the author (Adam Foster) a few years back, after Minerva was fully released IIRC.
I think everyone waited compatibility with the Source engine edition from EP1 to be resolved - as @daz said.