Milotic is all about stall. Hence, my movepool would probably be something like this:
Milotic@Leftovers
Bold Nature
Ability: Marvel Scale.
EVs: 252 HP, 126 Def, 126 SDef.
-Protect
-Recover
-Toxic
-Scald.
This Milotic set is all about walling the heck outta stuff, which Milotic does like a champ. It's typing is great defensively, having a mere two weaknesses. The moves almost speak for themselves: Toxic, Protect and Recover are self-explanatory, while Scald is to prevent Milotic from being taunt bait, and also provides an alternative status to inflict in case it does get taunted, and if you're lucky it can really mess up something like a Garchomp. Bold Nature is to maximize it's Physical defences- it already has enough special to not need a nature boost. EVs are split amongst HP, Defense and Special Defense. HP is to maximize Recover's healing, and I pray I don't need to explain the other two. Marvel Scale is Milotic's best ability considering outside of fast physical attackers like Garchomp, statusing Milotic is probably your best bet at not being walled by it, and Milotic can take advantage of that. Overall, Milotic will never be a top-tier threat unless it gets a Mega Evolution like Mawile's, but in lower tiers, Milotic is monstrously hard to take down- even the mighty Arcanine has trouble, although there are a couple of counters to Milotic.
Counters: Milotic's defense isn't THAT good, and as such my first check that comes to mind is Pikachu. Pikachu outspeeds Milotic, meaning Milotic CANNOT status it bar a lucky Quick Claw activation. If it tries, it WILL take a Volt Tackle to the face, and with a Light Ball, that OHKOes defensively invested Kyogres and Yveltals. Yeah, Milotic's not gonna enjoy that. Luxray and Electivire also come to mind, albeit somewhat less than Pikachu, seeing as they don't get access to Volt Tackle, which is amazing, and have to use the less-than-stellar Wild Charge instead.. Pikachu can also counter-status Milotic with Nuzzle, but that'd trigger Marvel Scale, and Pikachu DOES NOT want that.
Mega Venusaurhard counters Milotic. Leech Seed or Grassy Terrain, Milotic can't do a thing to MVenusaur, while it can just give Milotic a lot of grief. Other than that, however, there really isn't much that can actually check Milotic, outside of MAYBE Mega Absolwho can reflect Toxics back in Milotic's face with it's amazing ability of Magic Bounce.