Primarina can Work-Up -> Bloom Doom which beats Milotic in two moves. Milotic's strongest move against Primarina is Specs HP Electric, which doesn't 2HKO unless Milotic runs a lot of investment, at which point it might end up being slower.
Milotic can run Light Screen+Haze to beat this, however. But Primarina also runs the threat of Encore. I don't care to see how far the counter sets can go, but with standard sets Primarina would win because SDef Milotic is not a thing people use and Specs Moonblast 2HKO's, and most Primarinas are ev'd to outspeed uninvested base 80's.
