For Example, something I find to be a hindrance in Chiptune Music ( And don't get me wrong, its my opinion as a drummer ) Is the lack of control over the beat. Its repetitive and essentially if you don't have it prepared, the beat will stay the same. Playing live music with musicians, essentially jamming with friends, the drummer has the power to keep and alter the beat and structure. In Chiptune, there is no freedom in percussion, which bother me at least.
I don't perform live at all so all my concentration is on the creation part. Having a repetitive beat is more of a style issue rather than a limitation of chipmusic creation. As the genre has its roots in sequenced electronic music rather than live music with live instruments, beats might have a lesser importance to the composers than for example the melody. Disregarding the obvious limitations of different platforms, in creation, the limitations are what you choose them to be. "Chipmusic" is a broad genre than can encompass pretty much anything you want to do, from melodic synth pop to polka to metal to folk.
However, depending on who you ask, there are differences as to what people consider "chipmusic". For a hardcore oldschooler like myself, chipmusic means "music composed for an old low polyphony audio chip with limited capabilities" whereas for someone else it might mean just about anything that happens to use chippy instruments here and there. For me, if the creation involves MIDI in any way, it's not "pure" chipmusic 
Therefore the only limitations for me are the limitations of the software being used and the features of the used platform.
Not sure if any of this helps or not but anyway