1.) Critical hits (every tenth hit) ignore the stat boost offered by PES - so they will be deadly. Evolutions can generally take those crits much better. Moreover, they fear those new moves 'Mountain Storm' and 'Ice Breath'
Well, critical hits are part of game. +1 Salamence will break through most steels when Outrage hits for critical damage. So really strong critical hit most of time will take down Pokemon, even when resisted (except x4 resistance). However yeah, Mountain Storm and Ice Breath are problems.
2.) If these kind of pokemon are overused, and I guess this will be the case for some of them, at least at the beginning, one gets to see moves like 'knock off' more often again. But as an experienced battler, one can antipizipate these actions, so that's not a big deal.
I don't remember anyone saying "This is gonna OU for sure !" except few ones like Porygon2, Dusclops and maybe Munchlax, Golbat and Gligar (in case of last 3 this maybe is quite strong). And most of those examples were for lower tiers, as I think some of them may really find few niche and some of those ideas are interesting. But most of them in lower tiers, like many people mentioned IMO. But I'm sure that some of them will be totally niche, so in some cases you may be right ;).
I don't say that you don't make good points, because they are solid. But they were mentioned earlier more then few times by other people.
3.) Most of the pokemon hyped here lack a resistance against hail and sandstorm - especially the latter one will be absolutely deadly - you WILL see how useful Leftovers actually are. Sandstorm combined with Toxic Spikes or Stealth Rock and PES-Pokemon will face a quick death and can be considered as absolutely useless, including Porygon2.
True, however many of them has access to good healing move (Golbat, Chansey, etc.) making this Leftovers loss a bit less painful. And if you face Toxic Spikes (especially two layers) even good Leftovers walls can't handle them, if they're not immune to them (however they may live few turns more). But yeah, in some cases this additional Sandstorm/Hail damage may be extremely crucial, but remember, boost is huge (50%) so there must be some flaws. And weather weakness is one of them. But seriously it turns some Pokemon into interesting options. Maybe hype in some moments a bit too strong, however when you see how something like Porygon2 or Dusclops can handle hits, then you may be positively surprised.
4.) When calculating those base stats, it might be useful, at least for the majority of pokemon, to subtract 6% of all defense stats, too, since this is the amount of HP Leftovers give you back.
Well, in case of Chansey it's perfect example (I mentioned this) as in long run Blissey takes special hits better then Chansey thanks to those little Leftovers. But yeah, you must always count those Leftovers.
5.) Most of the pokemon have a fairly poor attack / special attack and only fulfil a specific counter/stall role.
And here I must say, that I see... nothing wrong with this. IMO if one Pokemon is great at one thing then it's better then good Pokemon in everything. You build a team around all 6 of them, and each one of them must fill their niche to compliment each other. If you need this one exact niche, then why not use this one certain Pokemon. True, most of them will be used on really defensive teams, however if you like to play for example stall (for example I like it) then you may love this much higher diversity in choices. Even if one certain Pokemon fill certainly small niche. As long as they're viable then it's really fine.
Porygon2 is really nice and has its niche, but on the other hand - it only fulfils this specific counter role mentioned. Without a STAB move and a really good special attack, any pokemon that resist IB or whatever can finally be switched in and set up. Moreover, being affected by sandstorm whilst being unable to hold Leftovers, will be a huge disadvantage for such a 'counter-only pokemon'...
But you may say, that this niche may be EXTREMELY IMPORTANT. Just look at those physical attackers - Salamence, Garchomp, Ononokusu, Dragonite, Rayquaza, Groudon... it's really hard to find good checks for all of them at once and Porygon2 may pretty much cover all of them, while having access to reliable recovery unlike something like Cresselia. I can easily imagine them dominate metagame (for example for 6x% of usage), so something like Porygon2 may be more usefull then we all think. True, it won't fit every single kind of team, however IMO his usefulness will be really good. But yeah, it really depends how metagame will shift, but with all those offensive behemots he may be a really important anti-metagame Pokemon.