Some points I'd like to make:
Deoxys-D: It's threatening, but very predictable and its strengths are easily overcome by simple methods. It's also set-up bait for a variety of pokemon (oppurtunity cost). 1. Can't sweep or wall significant portions, 2. Has oppurtunity cost, ie. pokemon can set up on it, 3. Can not perform multiple roles, it really has only one, perhaps two roles! - My opinion: S -> A rank
Dragonite: Let's be real here, this is THE 0 OPPURTUNITY COST POKEMON, if dragonite is out, there is NO such thing as a free turn, most people are busy trying to prepare for this in every team they make, it can sweep significant portions, it's ONLY flaw is stealth rock, it can set up in front of some offensive powerhouses AFTER stealth rock, Alakazam, Keldeo, Tornadus-T, to name a few. Requires minimal support, seriously, anyone clever who uses Dragonite has an ice/rock/dragon resist ready to set-up on the scarf attack that revenges him. Not to mention if you like, rapid spin support all-but guarantees a set-up chance. My opinion: A -> S rank
Thundurus-T: I think this is an incredibly overrated pokemon, its primary stab is easily checked, it's a little too slow to do its job and is SR weak.. It's easily revenged and has great difficulty setting up, if its scarfed, it wears out quickly. My opinion: A -> B rank
Ferrothorn: Lettuce be real tea here, this pokemon in B rank? it's only the most used hazard abuser and can literally sit in front of a lot of pokemon for multiple turns, it also makes a great fire/fight bait which you can switch a resist into. The only things that give this trouble really (with good teammates) are grass types/magnezone and clever magic bounce switch ins, as most threatening sweepers may check it, but not necessarily stop it from using its hazards. It gives away oppurtunity turns though, but is difficult to set up on, so my opinion: B -> A rank
Gengar: I'm torn here, this thing is amazing, and has always been amazing, but I can see where it fits into B in the sense that it gives away set-up turns a lot of the time to the dragons and Gyarados... otherwise I think it's borderline A for it's ability to check so many threats and even wall certain ones, not to mention it's incredibly difficult to switch into, except for very specific counters.
Gothitelle: Just wondering how it could be considered B rank, when it's so... mediocre.. I'd compare it to magnezone, although a less effective magnezone, I can see it has its perks, such as trapping Terrakion counters, but otherwise she gives away a lot of oppurtunity turns and is pursuit bait, not to mention very frail and very difficult to fit on a team, often a liability. My opinion: B -> D rank
Infernape: C rank.. really? it gives a hell of a lot of teams trouble and it's primary counters (specific psychics such as latias) are often dealt with by simple techniques (such as pursuit trapping for the aforementioned latias). Let's not forget its basically impossible to set up in front of infernape unless it's scarfed, and as for the scarf set.... I'm sure I won't have to sing its praises so you know how good it is. My opinion: C -> B
Edit: Nvm didn't see magnezone, B is a fitting rank, albeit it gives away turns a lot of the time (unless it runs hp ice, which allows it to sweep but often stops it doing its job such as reliably koing a scizor)
edit 2: Keldeo's problem is not that she can't break through enough walls, its that there are enough faster (or speed boosting) pokemon that can threaten her or set-up on her. The pokemon that do wall her (such as physical Gastro/Amoonguss/Celebi/Jellicent) also wall her effortlessly and are given free turns.. hence why she might be more fitting as a B rank pokemon rather than an A rank one.
edit 3: Hydreigon is completely outclassed, even as a jellicent/rotom-w/etc check it is outclassed most of the time by the lati twins or even kyurem. It has no way of boosting and is remarkably slow, scarf set is outclassed, life orb attacker is outclassed, substitute has its perks but is also somewhat outclassed, more easily walled or outsped than most special attackers. Perhaps the only way it stands out is as a way to deal with sun/rain/sand at the same time by being able to check various threats from each and its also difficult to set-up against. I would in fact say Hydreigon is borderline D rank.. but thats probably stretching it too far, my opinion: B -> C rank