Yeah, I used Eclipse for Java in grad school, but that was way too long ago. I remember using it for PHP and JavaScript several years later, until I got tired of the bloat. It seems like it's gotten better over time, but at that time I had changed to Geany, and eventually to vim, which I currently use for C, Python, JavaScript, Go, and pretty much every language I've done in the last decade.
As far as integration with the window decorations and all that, I use gvim, which is essentially vim wrapped in a gtk3 window with the traditional window decorations: it's perfect. I have to be honest and say that I've never tested any other non-gtk IDE in MATE to verify its compatibility... I should probably add that to my to-do list at some point to try to fix any gtk/theme issues 
