The problem with this entire comment is that you are only taking manaphy in the context of an entire meta, if the only thing you had to worry about in a battle was only manaphy then this comment would make sense, but that is obviously not the case, i never said there werent true counters in the game, i said they were pretty lacking, spdef unaware clef is indeed a counter, to which ive mentioned in my original post but that doesnt make manaphy balanced knowing clef can safely counter it, thats like saying kyogre is balanced in this pvp meta since shedinja and chansey can counter it, i shouldnt be forced to run one of these mons everytime so i dont automatically lose to kyogre, its clearly unbalanced. In regards to checking manaphy, i think you are underestimating its bulk quite a bit, as far as scarfers are concern i cant think of many that revenge kill it easily, breloom and serp seem to be the only ones i have in mind. Things like staraptor, gengar, rotom, drill and medicham are some examples of pokemon who cant revenge kill manaphy after sr damage. Things like specs lati, jolteon/raikou and weather abusers like kingdra or venu seem the most effective to check to it.
Scouting a manaphy set is very hard for any team giving its offensive pressure, yeah you can try to predict every move hes going for, but at +3, unless youre using stall (which manaphy easily just gets up to +6) everything is going to take a lot of damage, even bulky waters like suicune who cant do much back to manaphy, allowing it to get up to +6 and the only way for suicune to beat it is if rain isnt up, bulky rotom is 2hko by +3 surf after rocks and slowbro is the same thing as suicune and has to hope there isnt rain up. AV azu is an option but gets worn down pretty quickly with hazards/getting chipped from things like u-turn etc. Also its not really worth calling these mons true counters since they do not fully deal with manaphy's options and have to hope something like psychic/energy ball is absent in its movepool to deal with it, which most still do a bad job to begin with.
Sun teams do give manaphy a hard time, the thing is its not only manaphy you have to deal with, rain teams automatically give a better MU to manaphy (rain being a great choice for manaphy as explained in the first post), obviously MU like manaphy vs ninetales on the sun is bad for manaphy but with the help from rain, that is patched up very easily, and at this point you are now again pressured by manaphy, and with a potential setup tg against something like a darm or entei etc. makes it very hard for you to deal with, and now at +3 ninetales doesnt deal with it.
There is much more context you have to give regarding manaphy, talking as if its a 6v1 against manaphy is obviously easy to point out its flaws but thats is never the case.