I've used Alomomola extensively since the beginning of X/Y and I must say it has legitimate, niche uses in the metagame.
I would only ever suggest its use for support on defensive and stall teams. Bringing it into play instantly gives all momentum to your opponent and there is very little Alomo can do about it. (Compared to Audino, who can yawn to force a switch and give you a free turn to wish pass to something else) so it is highly suggested you run dedicated counters for whatever it may draw into play. (Unaware pokemon are a very nice compliment to it, as an Alomo wish will nearly always restore them to full hp, and they could care less about its opponent's boosts)
In my experience, Alo is best utilized as the physically defensive side of a cleric support core. It takes a lot of pressure off of, say, Chansey, who has no passive recovery and can not both heal itself and support its team simultaneously. Chansey alone trying to cleric for a team will get worn down after its third or forth time in the field, or become setup fodder while it takes the few turns it needs to patch itself up. With an Alomomola supplementing its durability it will be rare to not see it to the end of the game, no matter how many times it switches in and without having to take any extra time at all to keep itself lively.
As for sets, I've had a bit of experience with those, too.
My standby is:
General Sunfish@leftovers
252Hp/252Def/4SpD Relaxed/Impish
Knock Off
Scald(Toxic)
Protect(Refresh/Magic Coat/Mirror Coat)
Wish
-Generally you want to be as much of an inconvenience as possible to as wide a range of pokemon as possible. Short of Mega-Pokemon, Knock Off is always a relevant blow to your opponent's switch-in. Be it Life Orb, Choiced items, or Leftovers, they're going to be noticing the repercussions of that knock off for turns to come. And trust me, you really want to be able to consistently remove that Aegislash's leftovers.
-Not having Toxic as a mainstay of the set may turn some heads but, honestly, anything the sunfish could toxic and stall out, it could just as readily fish for a Scald Burn and stall out equally as well, with the added benefit of being able to burn certain steel targets that otherwise would make Alomo completely ineffectual. Running one or the other helps in removing status effect redundancy and ensures it always has something meaningful to cripple its opponent with. It also helps keep the fish from being absolute taunt bait. Nevertheless, if there is no other pokemon on your team that can completely stall out a roosting Dragonite, Toxic is there at your discretion.
-The third slot is where you really want specialization when it comes to your Alomo. Protect is the most general answer, as it allows for adequate scouting and for Alo to stall out a few specific threats it may struggle with. Refresh would be my second top choice, especially if you're running Alomomola without Heal Bell support, I'de have it over protect unless Alo is your only physical speedbump. Ensuring your fish is not randomly burned or Toxiced will greatly increase its longevity, and being able to out PP Toxic stall pokemon will let you win most battles of attrition. Magic Coat has its uses; generally you should be using your passive move on their switch and not sending your Alomomola in against a taunting pokemon, but in the rare instances where your hand is forced it can be a life saver. Mirror Coat works exactly like Counter Chansey with the added utility that you'll likely get Alomo back up to full hp later in the fight with some crafty switching while it's just doing its normal job.
-Wish is the bread and butter of the pokemon. If you're not using Alomomola for Wish support, don't use it.
If you're running Alomo with no team support what so ever, I would suggest the following with no variation. It will ensure Alomo stays around for as long as it possibly can, while still being able to status and stall out as wide a variety of threats as possible.
Mega Luvdisc@leftovers
252Hp/252Def/4SpD Bold
Scald
Refresh
Protect
Wish
General rule of play is you should be keeping in Alomo as little as possible. Bring it in, setup a wish, take it out. The more you keep it cycling onto your bench, the longer it will live, and the longer everything else on your team will live as well.
Finally, if you're utilizing Alomomola and surprised by how effective it can be, but want to carry over some of its more useful benefits (support without losing excess momentum) to a more offensive oriented team I highly suggest your try an Audino Cleric set. 252 hp/ 252 defense of choice and regenerator supported wishes and heal bells, with the added benefit of not being setup fodder like Alomo thanks to Yawn.