Natures of VC Pokemon are determined by the number of Exp. Points they have when you transfer them into Bank. If you want a Timid nature, make sure you give it a total that ends in 10, 35, 60, or 85; if you want Jolly you can use 13, 38, 63, or 88 instead.
EVs have no effect at all on shininess, and are zeroed out on everything that moves VC->Bank in any case. Only the IVs matter, and several types of encounters are incapable of putting the random seed into a state where it can produce a shiny IV spread at all, but fortunately static encounters like Mewtwo are one of the few methods that leaves everything available without spending extra effort to edit things after the fact. On a freshly caught L70 Mewtwo, the only way it will be shiny upon transfer is if it starts with a Defense stat of exactly 145, Speed of exactly 201, Special of exactly 234, and Attack at one of the following values: 161, 163, 167, 168, 173, 174, 178, or 180.