I think Latios is the one that needs to be S rank. He's just incredibly powerful with a choice specs and even tyranitar will have to think twice before switching in on that. Blissey can be 2hkoed by psyshock and offensive heatran is taken out by surf. Now Latios suffers a bit from four moveslot syndrome (Trick vs HP Fire) when using a choice specs, but they both cripple Ferrothorn and Jirachi badly (both are 2hkoed by hp fire and they both hate trick.) he can also resort to a Life Orb (which I think is his best set because he can switch moves) and still be very threatening offensively. Or he can go on a support route with Memento and dual screens (which is not outclassed by latias because Memento > Healing Wish imo) and an offensive calm mind set which once again is not outclassed by his sister. He can even go on a physical route to take out Tyranitar with +1 earthquake or be a good revenge killer when having a choice scarf (Draco Meteor is still going to hurt).
Nothing can fully counter all of his sets and he is just so versatile. He truly deserves S rank.
I am sorry if I sound like a complete jerk,but your post looks like its a Smogon Latios analysis overview with all the negatives removed XD.
Anyway,I have never had any problems with Latios,and maybe thats because I am a sand-balance exclusive player,but maybe it is because it's Choice sets gets Pursuit trapped too easily.I mean,the first thing that goes on in your mind once you see a Latios in your opponent's team,is "I HAVE keep my Pursuit trapper alive until Latios is dead".Pursuit trapping it isn't really that hard,just bring your trapper in after it's Sp.Att is halved.
Now being a sand-balance exclusive,I tend to run Scizor and Tyranitar a lot,so maybe I am being biased.Most common steel-type Dragon checks,including Ferrothorn,Jirachi,Bronzong,Scizor,and to a lesser extent,Skarmory and Forretress,can all check Latios decently well (yeah.....Forre and Skarm can't really take a hit),and if you are indeed running a non-offensive team,dedicated Dragon-type checks are mandatory.What I am trying to say is,Latios's checks are no different from any other Dragon-type in OU,making dedicated checks to Latios not worthwhile.For example,compare it to Keldeo,people HAVE to run something that resists Keldeo's Dual-STAB if they don't want to be screwed,and even then,it still gives some trouble.
You said that Latios can get past all it's counters with the appropriate moves,and while that is not completely correct,I do kind of agree.But then again,it is a Dragon-type,and every other Dragon-type in OU can do this,not just Latios,so if Latios gets sent to S rank,the other Dragons might a well do too.
Take Dragonite for example.Just like what you said about Latios,it has extremely high attack,has the ability to run multiple sets(DD,Rain Abuse,Rain Tank,Multiscale Shuffler,Mixed,etc.),and get past it's counters with the appropriate move.For example,it can get past Ferrothorn,Skarmory and Forretress with Fire Blast,Heatran with EQ,it can 2HKO Air Balloon Heatran with +1 Outrage while it can't OHKO back with Multiscale intact,OHKO or 2HKO Landorus-Therian,Gliscor,and Hippowdon with Ice beam (or Waterfall or Aqua Tail if it gets it).Unlike Latios,it cannot be trappped easily,and even 2HKO some steels with Outrage.Does this mean Dragonite is S rank material?NO.Just like Latios,it has some crippling flaws that always get in the way.For starters,a Stealth Rock weakness and susceptibility to priority and revenge killing even at +1 due to low speed.
So overall,Latios is just like other Dragons,very low checks,versatile,powerful,but with exploitable flaws.So if it goes S rank,the other Dragons might as well.