One limitation I do know is that, in a big project, with a lot of images, it is prone to crash due to a windows limit on how many images files can be used by a program, or something like that.
there is I think an option to turn off icons to prevent this, but then again this is for very large projects with tons of objects that contains images.
Also keep in mind this engine is thought for browser games first, and every export method (appart from cocoon.io as far as I know, and for iOS also) is basically a packaged version of chromium, I prefer to let you know that rather than being dissapointed, that does not mean it is incapable of handling large projects, it simply means it can be harder than expected.