I think part of it was that I had basically memorized all the keystrokes for the MathType editor, and most of them didn't work in the MS Equation editor, which annoyed me. Also, I had issues with parentheses formatting correctly but I suspect that's been fixed in the last 15 years.
Still, I really do prefer to work with Markdown in general. The Markdown -> Pandoc -> LaTeX rendering just ends up looking prettier in my opinion, and at this point I'm pretty useless in any editor that doesn't have Vim keystrokes. Pandoc irons out the parts of LaTeX that I really hate (the `` vs " being the thing that's given me the most headaches), while letting me drop into raw LaTeX when I need it; not even getting into the fact that there's just math stuff that (as far as I know) doesn't work in Word or MathType's equation editor (e.g. bussproof trees).
I do get pretty annoyed when people try and tell me that regular LaTeX is "just as easy" as Word, because even as someone who has a reasonably good handle on LaTeX I can say that is just not true. TeX is arcane and weird and annoying and inconsistent, and I don't blame people for using Word compared to it.
Pandoc was a game changer for me. I picked up LaTeX equation editor pretty quick, and being able to write markdown was so much more pleasant in my mind.
It’s not perfect; tables are a pain still, but I have no desire to go back to Word.