In theory, cof would be great against mega mawile. In practice, not so much... Mawile just rails cof if she goes for an SD and you still won't outspeed. At that point, you can kiss cof good bye. Cof does take kan perfectly because kan's boost is via PuP so you can always count on taking kan at neutral or +1 at worst (scrappy PuP)
Anatya, I see you're looking into stopping mega lucario. Yuttt and I actually have been competing to find who could stop it best and we came up with three counters: Mega venusaur (mixed investment, not great at living [2hko itt if not max def] but can eq, Gyrados w/intimidate [resttalk set], and Slowbro (max def/hp invest). Slowbro/Gyara worked perfectly and we've been running them ever since on our teams. I don't have the calcs, but I guarantee both will live +2 hits well. DTC seems to agree with Yuttt on running gyarados. I'mm just use venu (specially invested now) to take care of special luc.
Personally, slowbro is better because if I don't get a burn, I can switch out to cof/venu/skarm and get that regenerator bonus going for me.
Other issues with megas include all the wall breaking megas this time around. They are huge detriments to stall, most noticeably mega chomp if it goes mixed, mega pinsir, mega kan and occasionally mega mawile. My team has checks/counters for most as I've spent 13 days with that RMT up working those kinks out.
To note, stall is a very tough style to run right now. We're having trouble running it well, winning only about 75-80% of the time any more. This is down from the 90-99% that we had in gen5 (Yuttt topped the ladder in 5th before going provisional again and gave up, I had never gotten out before getting into the top 30). If the wall breakers leave a bit, we can truly get down to stalling again.
Interesting to note, neither Yuttt nor I currently run fairies. They aren't bad, but as a rule of thumb, most dragons that go for set up sweeps are physical. Therefore, faeries really got wrecked by a coverage move like EQ or iron head... Freaking kyub... Really, faeries being limited physically is a death wish. MG Clefable seems to break the mold a bit, but I still found her underwhelming, filling in as a great outrage stopper and perfect hydregion counter but not much else.
Speaking of which, MG clefable is something stall teams need to prepare for. That stupid thing is everywhere and when it's 1v1, you can't phaze it. I suggest a flash cannon/iron head somewhere. I run skill swap to take care of it, so I can status stall it.
Megas we've attempted in stall are limited. Mega venusaur and scizor are our two go-to's, though it seems like blastoise wouldn't be bad. We selected the two we did for recovery, however. Both pokemon work very well, though again I prefer mega venu for his monstrous bulk on both sides.
Contrary to my belief at the beginning of 6th gen, the meta game went physical. I thought Willowisp's acc would cause a shift towards special sweepers. This, however, didn't happen. Lovely, because you basically have to run three physical walls and another mixed-leaning-physical wall to make sure you've got all those threats covered.
Clerics hate mega gengar. That is all. If those users were smart, they'd just constantly show an attempt to mega evolve on a cleric just to keep it out the whole game. Since most of us probably run fairy/chansey as clerics, it is rather hard to get in one sludgebomb/perish trap gengar to support the team. Florges, however, can run psychic to alleviate this ever so slightly (or at least lure before the mega evol)
I see a few complains here or there about defog. I actually like defog, running it on my skarm. It is wonderful simply because HO STILL suicide leads. Take care of it and then defog/sr with skarm at some later point. I don't suggest extra hazards on stall, Web is pointless, spikes take too long and are too easy to lose and Tspikes mess up status stall teams. Rocks do their damage over time and still give you a fair return for causing switches imo.
56k mentioned heatran as a neccessity. This is true, and though he lacks recovery, there is nothing wrong with using a fairy to wish pass (fight resist to weakness, poison weak to immunity, steel weak to resistance) or even just run rest on him. The sleep mechanics allow for some maneuvering if you can't get to a heal bell user.
For pinsir, we've compiled a list of about 3 pokemon that can reliably take him on at +2. Zapdos, Skarmoy, Bronzong. Short list, eh? Rotom-w kind of works, and Lunatone is an idea of mine should I ever need an odd choice, but you need to resist that flying stab and then avoid the EQ hit as eq hits all flying resists for SE damage.