I think it depends if you want to use it with a Megastone or not. If you give it Mewtwonite Y, it'll be at base 140 speed > Darkrai's 125 speed, which means it'll outspeed Darkrai even with a Modest nature if its speed IV is high and you give it max speed EVs.
If you want to outspeed Darkrai but don't want to use a Megastone, you can Scarf Mewtwo and use it as a clean up sweeper.
However, having said all of that, competitively, Darkrai is frequently holding a Focus Sash, so your Mewtwo will most likely be put to sleep with Dark Void or KO'd by a Dark Pulse. Additionally, Dakrai is really uncommon in wifi battles in Gen VI considering that Pokebank is not open and there's no legitimate way to get Darkrai other than transferring.
What would be more important over wifi is out speeding Mega-Gengar, at base speed 130. If you're in battle with a Gengar and you both Mega-evolve, Mewtwo will be faster because all stats except speed are Mega'd on the first turn. If you switch into a Gengar before mega-evolving, you might have problems out speeding it, especially if your Mewtwo has bad speed IV.
There are other threats too, like Mega-Alakazam, Mega-Aerodactyl and Mega-Manectric, which will outspeed Mewtwo & its Mega forms.
Keep Modest Mewtwo if it has perfect speed IV; Gengar can be bred and therefore will most likely have perfect speed IV.
