i have never had huge problems with keldeo or thundurus-T to be honest. they're big threats to be sure but not markedly more so than the other things in this game. vs thundurus, handling NP is a very risky art, but so it is for any +2 boosting sweeper. i tend to incorporate a lot of phazing into my teams so i can handle it. keldeo's flaw is having stabs whose coverage sucks too damn much, and really people are not running it in rain as much as they should be (otherwise how can we explain its low-ass usage?). +1 rain hydro pump from keldeo is pretty beastly when you can't bring in chansey, but i find that the things that check keldeo best (amoong, latias, jelli) slide their way onto my teams naturally so i usually have a solution.
vs tornadus though, you basically have to kill everything else on the team and then kill it once it's the last mon. regenerator makes it astoundingly difficult to kill. it is wallable, but every time you think you've hurt it, it just uturns away and all your hard work disappears. bloody infuriating to say the least. also, chansey is not a solution to superpower tornadus. i am sick of hearing that it supposedly counters it, when it will definitely lose in the long run. chansey cannot switch in on superpower repeatedly. if you run enough phys def to not be 2hkoed after hazards, you will get washed away by +1 hydro pumps from keldeo and toed and their ilk. with no leftovers, it is basically always a fight you are going to lose. in other words, chansey is not a standalone solution to tornadus-T, the way sdef jirachi usually is. granted, if you play wisely and never switch chansey in on a superpower (only start taking superpowers after you're in safely), you can generally handle it. blissey gets floored by superpower so no conversation to be had there lol
and as for hydreigon, haxorus, mence, mamo, etc. a stall team should really have a plan for all of them, but damn it is tough. broad, powerful neutral coverage is really the name of the game in counter-minded play right now. just look at things like terrakion; my tentacruel sure as hell does not like coming in on LO stone edge.
mamo's strong ground/ice is surprisingly difficult to deal with - the best solution for stall is generally phys def skarm (if you run specially defensive spreads, you take just under half from icicle crash, so you'll lose to flinches and hazards - trust me, it happened to me ALL the time until i switched spreads). bronzong is boss but gets worn down way too easily (RESTALK BRONZONG LETS GO). in addition, bronzong is one of those bulky-no-utility mons i was talking about earlier - the ONLY useful thing it has is stealth rock. phazing? nope. spinning? nope. it doesn't even get heal bell, yet it's a FREAKING BELL
haxorus is a powerhouse, but its problem is that stall will generally incorporate a solution to it in the process of finding a solution to something else - it's powerful, but not the kind of threat that makes me say "okay shit i don't have a plan for this". physdef skarm handles it quite comfortably as long as you're careful about +2 rain aqua tails n shit, and if you're in rain you got bigger problems to worry about.
chansey can generally handle hydreigon, but it's a losing battle for both of them - hydreigon hurts chansey deeply with superpower but really will almost never 2hko it, and unlike tornadus-T, it cannot be a lasting threat unless it gives up turns to use roost. that means i can generally counterstall it if it tries to wear me down. watch out for taunt/roost stallbreaking sets though, those are hell and you basically autolose to those. thank god they're so damn rare
the problem with mence is mainly that you generally have to sack something to scout it, because there is no one mon that counters all the sets, and chances are the sack gave it a moxie boost that now makes it uncounterable. such is life. even stall needs to have checking techniques sometimes. the problem there is that if you run a dedicated panic-button check mon (eg alakazam, scarf rak) on stall, you just lost a slot that you crucially needed for defensive synergy. now you're building a stall team with one mon down, so your check basically has to handle a loooong ass list of boosting threats. otherwise it's cost you more than it's worth.... either way you lose to something lol. running a dedicated panic button like that would probably reduce your need for phazing and toxic (both of which specialize in countering boosting sweepers), but you still lose out on a bulky defensive option that you kind of need in a team type like stall, that's so hard to use right now.