Simply this: There are other (better) Pokemon out there.
Yeah, I admit, Shaymin Sky is pretty impressive, but most of its powers depend on Serene Grace. Also, a total of 600, while quite good, is nothing compared to more than 15-20 Pokemon boasting of 680 Base Stats, and a whole TON of mega Pokemon. These Pokemon, like Rayquaza, and ExtremeKiller Arceus, they pack a huge punch, and they do massive damage. And they are fast. Let's face it, without a Choice Scarf, Shaymin cannot outspeed the likes of Rayquaza, etc. A choice scarf locks it into its move, and given that Grass doesn't have as good coverage as say, Fire, or neutrally effective Dragon, or even the new Fairy type attacks. Its main STAB is also countered by lots of Pokemon that are 2x or even 4x resistant to Grass (Looks at Ho-oh, and Lugia).
Seed Flare is negated by Ho-oh/ Multiscale Lugia, and Protean Greninja kills it before it can become a threat.
That said, it can abuse its powers, but hey, in the long run, other Pokemon prove more effective. A few months ago, Shaymin Sky was quite active, and now, due to Primal Groudon/ Kyogre and the new race of Mega Pokemon, it just lost its place to the competition.