Have you played this meta? There's stuff faster than Weavile literally everywhere. Mainly weather sweepers. Sand Rush+Sand Stream Tyranitar / Excadrill, Desolate Land+Chlorophyll Venusaur / Victreebel, Swift Swim / Primordial Sea Kingdra / Kabutops / Ludicolo / you name it. Apparently somebody's using Chlorophyll Ninetales although I'm pretty skeptical about that set in this meta given the prevalence of the "harsh" weathers. But yeah. Even discounting Speed Boost and dragon dancers, Weavile is outsped routinely.
Most of them can't switch into Weavile, and most of them lack the longevity to appreciate having to tank a Fake Out before it switches. Venusaur and Victreebel can both recover decently, but they're outright weak to Ice.
They can revenge into it, of course, but that's less than ideal.
My current team has no trouble with Manaphy at all. Given how insanely good both Desolate Land Raikou and Desolate Land Heatran are and the fact that they both just kinda dump on Manaphy it is pretty easy to deal with in general for a well-built offensive squad.
As for defensive/balanced teams, they have plenty of methods of dealing with it well; just off of the top of my head things that can handle it on defenisive teams include CM+BoltBeam Blissey (which is able to come in on it and use it for setup bait on semistall and it isn't even like it's difficult to stay healthy enough to take it on when pivoting through stuff due to Regenerator being insanely good), Qualot Suicune, specially bulky Water Absorb/Desolate Land 'mons which aren't beaten by Ice Beam/Energy Ball/Psychic (these aren't hard to come by either, with Heatran being the most obvious example), Ferrothorn (has an all-around easy time taking it on due to it's typing+Regen), Qualot+CM Clefable and SpD Qualot cleric Clefable--among other things.
Basically what I'm saying is that I don't see Manaphy as a particularly restrictive force in the meta to the point where it is banworthy, and given that a: offense is the best/most consistent playstyle in this meta and b: that defensive and balanced teams have a plethora of options to handle it, I don't see it as problematic at all.
Specially bulky Ferrothorn can't OHKO Manaphy with Power Whip.
4 Atk Ferrothorn Power Whip vs. 0 HP / 4 Def Manaphy: 246-290 (72.1 - 85%) -- guaranteed 2HKO after poison damage
(Poison is simulating Leech Seed damage)
Manaphy can literally just Rest stall Ferrothorn and Tail Glow up to murder it.
252+ Atk Ferrothorn Power Whip vs. 252 HP / 4 Def Manaphy: 342-404 (84.6 - 100%) -- 6.3% chance to OHKO
Bulky Manaphy vs Adamant attacking Ferrothorn is actually at risk of being KOed, even without Leech Seed, but repeatedly switching into Scald is going to get it Burned at
some point, and then Manaphy can go back to Rest stalling it, which takes no time at all since Power Whip only has 8 PP anyway.
Ferrothorn is a dubious check to Manaphy.
Unaware Suicune takes up to 40% (Assuming Physically Defensive) damage from Energy Ball, and can't really do anything to hit back until it's significantly set up. If it switches into Energy Ball, it
has to immediately Rest and then hope it gets lucky with Sleep Talk -and that Manaphy
doesn't get lucky with Special Defense drops. Also, it can't really do jack to Manaphy anyway.
+6 0 SpA Suicune Scald vs. 0 HP / 0 SpD Manaphy: 157-186 (46 - 54.5%) -- 57.4% chance to 2HKO
If Manaphy is instead bulky it can't even be 2HKOed at
+6. (And hoping for a Burn is futile because Hydration will instantly clear it) This means it can literally Rest stall through all of Suicune's Scald PP -and Sleep Talk is
not going to optimize PP usage. You're going to see Scalds being wasted early on, before you're substantially boosted, which means even
non-bulky Manaphy may well be able to Rest stall Suicune.
Clefable being a shaky check to Manaphy was
already addressed by someone else before you posted.
Desolate Land-based checks run into the issue that Manaphy can then switch back in to clear your weather and gain the ability to nuke you, and usually suffer more from Stealth Rock than Manaphy does, whether from actual vulnerability (eg Chandelure) or from a complete lack of recovery. (eg Heatran) Water Absorb is more stable, and prediction can even make up for a lack of recovery, but they're still shaky -I'm
using Water Absorb Heatran and it's just not that effective. (It's
Specially Defensive and it takes 40% from +6 Psychic) Desolate Land Raikou is a solid stop to it -for an
offense team.
Calm Mind boltbeam Blissey works, yes, though even then...
+6 252 SpA Manaphy Scald vs. 0 HP / 252 SpD Blissey in Heavy Rain on a critical hit: 627-738 (96.3 - 113.3%) -- 75% chance to OHKO
... if Manaphy gets
one crit anywhere in there, Blissey is dead if it's not Unaware.
None of those is
really a stable stall check to Manaphy.
I also dispute the claim that offense is the best/most consistent playstyle. My own experience is that stall is a lot more stable, just like it is in most metas, you know,
except for Manaphy existing.
EDIT:
Confirming I reached top 15 on ladder. I'll probably climb higher later, but whatever: I didn't want to reach #1, then fall to sixteen before I remembered to take a screenshot.
I'm
pro ban, and I've already covered the general shape of why: there are almost no answers on stall, the answers there
are range from shaky to "lol not really", and it's not like Manaphy is useless against non-stall teams or something. Many proposed counters aren't actually counters at all, or Manaphy can simply outlast them until general chipping takes them out/puts them in a place where Manaphy can finish them while Manaphy remains pristine. Furthermore, some of the closest counters to being reliable are overly narrow/specialized at the job, with dubious viability against the rest of the meta. Most of the traditional checks to a setup sweeper like Manaphy don't work at all or are very shaky -it's difficult to find an Unaware 'mon, even with Unaware possible to freely pass around, that can actually shrug off Manaphy's Scald+one coverage move, it's too bulky for powerful priority options to necessarily revenge into it, most of the things that
can outspeed it and grab a OHKO can't
switch into it safely, phazing it out doesn't help that much when it can set up so easily and heal off repeated chipping damage effortlessly...
It's just not healthy to have a Pokemon in the meta that can only really be dealt with safely/at all if you can outspeed and OHKO it
while being able to switch into any attack -especially since Scald's Burn chance means anything that isn't immune to Water or immune to Burn further constricts what options are viable at the task.
