as the introduction in the artscroll says, the reason shkulim was included in the cycle was because the vilna shas used to print shkulim with bavli. the cycle is based on what the printer included in the volumes and what it did not.
with respect to yerushalmi aramaic versus bavli: (1) as stated before, aramaic was the language of israel in those days (see, mel gibson, passion of the christ) (2) as stated before, the dialects differed.
it is also important to note that both gemaras are essentially a collection of peoples notes. the notes collected for yerushalmi were reprinted in a form much closer to its original. there was less editing. hence, yerushalmi appears in shorthand.
as stated above, the bavli went through extensive editing over the years and evolved to what you see today. the yerushalmi is less evolved.