My take on manaphy is that it is a good pokemon. Base 100 all around isnt anything to scoff at, and pure water is a great type. Setup has always been really nice for beating stall teams before manaphy, and after. But, as most setup mons deal with, manaphy has 4 move syndrome. There will always be some type of fat mon that will be an annoyance for manaphy sweepers, and there is no helping it. A Cm/rest/scald/rain dance set that is bulkier will auto-lose to grass types with leech seed and grass stab(namely giga drain) or some type of water immunity (storm drain, water absorb, dry skin), and a cm set without rest or rain dance loses survivability. These are the 1v1s though, which is not always enough to consider a mon bad or good definitely.
Archetypes of teams are meant to check each other, and each archetype is at some inhererent advantage/disadvantage vs another. H.O. teams have a disadvantage vs weather, Stall vs Setup, weather vs stall, balance vs H.O., or something along those lines ( and by no means are any of these right because I said so, but rather an example of existing archetypes I believe have these inherent +/- vs other teams). This doesn't mean by any criteria that H.O. CANNOT beat weather and whatnot, but it is harder to. The factors of leads, reads, and set choices are too varied to apply to a paper analysis of manaphy. In this light, it is a lot harder to be able to decide how to deal with the issue.
Balance Setup, for an example, running a Timid 3 attacks TG mana vs H.O. Manaphy is thick, but it isn't dummy thick, which, in my opinion, gives H.O. an inherent advantage when manaphy is in. Your balance core will usually get overwhelmed by the H.O. and not given a chance to heal/properly check the other team. Unless there is 0 priority and no mons faster than manaphy, it isn't going to have the chance to tail glow to effectively fill the role of a sweeper.
Team preview is meant to let you gather your thoughts on how to handle what you think the opponent's team is, and assess what members of your team will be win conditions, and how to meet those conditions. That is, what I believe to essentially be, competitive pokemon.
Whether or not you want to use your favorite archetype, the point is, your favorite archetype will not always be meta. There are competitive archetypes that are more suited for beating others that aren't as geared for that. When you pick up an archetype, you should learns the ins and outs, and what you want to incorporate to not lose to another archetype. You should also know what that archetype will have a disadvantage against, and not call for a ban because you lose more often than not. Stall and bulkier teams will inherently lose to manaphy because they cannot help but lose no less than 2 to 3 mons against a boosted move. This also applies to picking the pokemon for the archetype. There will be sets of mons that will be automatically useless on team preview, and may not be utilized in a match unless the counter(s) are taken care of. You should not only know that those counters could be encountered, but also if, and how, you can properly deal with that counter(s) and their support.
Overall standpoint : Don't Ban.
edit: just some spelling checks