The move from GTK2 to GTK3 is a significant change, but a necessary one. It's largely down to external factors out of an official flavour's control. MATE have completed the move to GTK3 on their roadmap, so versions after 1.16 are GTK3 only.
The development of GTK (by GNOME) affects the whole Linux ecosystem in general. You may hear of complaints like GNOME's massive simplification in their UI and themes breaking far too frequently with new GTK 3.xx versions.
Kudos to the MATE team for doing the monotonous job of updating the toolkit. 
Even if GTK3 isn't as "great" as GTK2, it's the latest spec developers use for writing Linux desktop apps (there's also Qt). I personally will stick with 16.04 for its life cycle. It's subtle things, but noticeable to GNOME 2 fans which is what that topic is dedicated for. 
There is some good to GTK3 - Ubuntu MATE 16.10 onwards supports HiDPI displays, and the codebase has common ground with upstream GNOME. Some say that by GTK4, GTK3 will have stabilised to that of GTK2 today, which is now in maintenance mode. 