I'm going to try to play devil's advocate on Manaphy. TBH I don't really care if it gets banned, but I do want to see points addressed for both sides instead of only the pro-ban arguments that we have now.
Here's the problem I see with banning Manaphy: It doesn't help the metagame. A true banning philosophy is something we should've set up a long time ago. The problem with current banning is that we can't abide by OU banning philosophy, because if we did, we would be constantly banning the many things that define ban-worthy in OU. Ubers banning philosophy doesn't help either, because then we are left with excessively broken threats in the metagame. We need to be somewhere in the middle. Ban-worthy mons like Zygarde can't really be labeled as ban-worthy because we'd almost always have ban-worthy mons in our metagame, so we need to figure out how to define broken.
For me, the most important aspect of banning something is "is the metagame more fun to play without x than with it?" I find this is a good benchmark for OMs, regardless of whether or not something is banworthy, for example, Imposter in BH. It's most definitely broken by most measures, but the metagame is better with it than without.
The experience for me in the non-manaphy metagame wasn't nearly as fun as with Manaphy. Manaphy tends to make life easier for offense, having more flexibility around such a reliable sweeper - however Manaphy also restricts offense in that it has to run viable revenge killers to handle it. This means we can't really tell whether or not this change nerfs or buffs offense without testing it, which is why the suspect test was a good idea. Now, from my experience, the lack of manaphy in the tier is freeing up teamslots on offense, and LESS SO than stall and balance which could afford to run Manaphy checks to begin with. The ladder has been much more heavily offensive, and a lack of great sweepers means that most teams consist of 5 fast, hard hitters and one support mon for hazards and/or control. Or in some cases, one sweeper. This is NOT conducive for a balanced metagame. Manaphy, which isn't an outrageously metagame warping threat as is, seems to help the playstyles be balanced, which is a good thing.
In the long run, I don't really care for manaphy, but I think its important for us to look at the situation the metagame faces - is this metagame better than the non-manaphy metagame, REGARDLESS of whether or not its broken?
"Fun" runs into the problem that different people find different things fun. I've found Manaphy unfun, period, having to face extremely tense situations where if I make a
single error, match over, I lose, Pokemon count irrelevant, everything else irrelevant, and it's
really hard to say what the right answer
is because Absolite and Sceptilite require entirely different answers
and it also matters whether Manaphy chooses to Tail Glow or lob a Scald -if it does the latter, a Red Orber is a free switchin, while if it does the former you're probably better off either attacking or switching in an -atespeeder. I'm sure there are people who find Manaphy contributes to making the meta fun because they personally like having a powerful setup sweeper that isn't held back by any major Achilles Heels.
Fun is the goal, yes, but using it as the direct metric for deciding a ban/unban isn't very
helpful.
During the period in which Manaphy was banned I saw an
increase in team diversity, personally, because now people didn't need multiple checks to Manaphy on literally every team to not be auto-killed by it, which was a problem given how little constitutes a check to it. Pre-ban I kept seeing the same Pokemon across teams, over and over again. Post-ban Red Orb stopped being a
given on any half-decent team, and I saw fewer cases of Entei+Zygarde -more teams carrying just one or the other.
I've also seen in increase in the variety of setup sweepers, rather than most any team running Manaphy with maybe a Physical setup sweeper if they were running setup sweepers at all.
As far as I can tell, by all the metrics (Except maybe "fun") you're talking about, Manaphy makes the meta worse, restricting play to an extremely narrow set of options if you want to function at all, while doing nothing to check any other egregious problems. (It's not like it restricts how influential -atespeed is, given that -atespeed is one of the only halfway reliable answers to it!) Offense is literally stupid for not running Manaphy and is even stupider for not running double -atespeed to
check Manaphy and is probably also stupid if it doesn't have a Red Orb somewhere in there, preferably one that isn't Primal Groudon so it actually resists Grass/Ice. (About the only nice thing I have to say about Manaphy's apparent influence on the meta is that it drove Primal Groudon out of popularity) That's 4 out of 6 teams members basically already defined for an offense team, and it about describes what I
saw from offensive teams before Manaphy was temp-banned.
I also think it's worth evaluating Absolite's impact on Manaphy (not suggesting an absolite ban, of course, but rather that Manaphy is the clear best user and it gives Mana a huge amount of versatility outside of wallbreaking/sweeping). I've found that even supposed counters can become very threatened by Manaphy pivoting in because of Absolite. As someone who used Absolite Starmie, Gengar, Keldeo, Celebi and Latios regularly during the period Manaphy was gone, I can honestly say Mana is much better at taking advantage of the stone's boosts than any given one of these (offensive magic bounce users being very different from defensive!). If Absolite Manaphy is on the cusp of being broken, why wouldn't other sets push it over the edge?
I bolded the last sentence because I'm not sure what it is you're trying to say there. I think you make good points overall, I just don't know what this last sentence even means.