I got a Shiny Thundurus on the GTS last night and it's obvious that it wasn't RNG'd or hacked because it has a neutral Nature and its IVs aren't perfect (seriously, if someone were to hack or RNG this thing, it would be perfect).
Seeing as though the Trade Board doesn't care about anything unless it's flawless, it's kinda hard to figure out what it's worth there. I mean, a Shiny Thundurus is probably more rare than one with a Timid Nature and max Speed IVs, right?
I was once modded for illegal activity because I made a topic asking for advice on nicknaming my Pokemon. 3DS FC: 5043-2277-6391 - THIEF
I got a shiny Thundurus on GTS as well (albeit it was Naive natured with 3 perfect usable IV's) but it'll still be worth something on the trading board to the right person. Personally unless you really don't want it I'd just keep it if I were you OR put it back on the GTS for say a tornadus and then put the tornadus on the GTS for another Thundurus (Or go straight for Thundurus for Thundurus) until you get a Thundurus with better nature and IV's,