SpD Tar is not a new check
SpD Scizor is not a new check
Jirachi is not a new check
Metagross is not a new check
Tornadus and Thunderus are not checks at all, they are OHKO'ed by Draco Meteor, and 2HKOed by any common move Latios carries, except maybe HP Fighting for Tyranitar. They cannot OHKO Latios either.
Starmie is not a check. See Genies, except Surf does not 2HKO Starmie.
Ferrothorn is a check, but dosent stop Latios coing back in later, and taking another 30~40% out of it. Or predicting it and using HP Fire, which it should carry.
Escavalier just forces it out, and even then, only on a DM. Surf will ruin it.
Tl;DR: Latios only gained two, shakey checks [Both are countered by HP Fire, which IMO, all Latios should be running, as it ruins 3 'checks' and hits Metagross and Jirachi hard too, ESPECIALLY in the Sun]
Gen 5 also gave Latios no counters, and removed Blissey as a Counter, due to Psyshock. It also removed Snorlax as a check. So, that's a net gain of +1 Check, and -1 Counter.
And there's other sets besides Specs too. Calm Mind Latios can take advantage of the switches caused by Specs Latios, for example, and can switch moves, while retaining the same power as Specs Latios [You CM on the switch it forces]. Or Life Orb Latios, who could carry Recover.
When did you ever see SpD Tar, SpD Jirachi, and SpD Scizor commonly run back in Gen 4? Very rarely, and most definitely not to the extent that they are now. For the purposes of this argument, they are "new" sets and checks.
Starmie can come into Surf or HP Fire with relative ease to threaten Latios. Also, HP Fire does not OHKO the genies even with SR, nor does the rare HP Fighting obviously. Meanwhile, Specs Hurricane will often OHKO with rocks, Thundurus can priority TWave, and Starmie's LO Ice Beam does upwards of 70%. Starmie is pretty good, though the genies are relatively shaky and I'll admit they are more revenge killers than anything else.
Why are you upset that Latios can switch out and hit Ferrothorn again later? That is the name of the game, and various pokemon can do this. Infernape can hit Tentacruel with Close Combat, switch out, and do it again, but does that make it broken? Heatran can Fire Blast your Specs Latios switch-in, switch out, and do it again, but that doesn't make it broken. You mention how it crushes steels with HP Fire in the sun but neglect to mention how they deal with Latios far more easily in the rain? Nope, no bias there.
For the nth time, the "but it can predict and use HP Fire" argument really needs to be thrown out the window, as it is exceedingly weak. I could just as easily have predicted your Latios switch into my Rotom and Thunder Waved, or known that you were going to bring Latios into Heatran's Fire Blast and used Dragon Pulse instead. So from now on I'm just going to stop replying to the prediction argument and only address the valid points in an argument.
Specs Latios isn't running all of Draco Meteor / Thunderbolt / Surf / HP Fire / Dragon Pulse / Psycho Shock / Trick at once. DM / Surf / HP Fire are the standard with the last slot for coverage - without PsyShock, Blissey will win, as is the case if you lack Trick. If you lack Dragon Pulse, you lack a STAB for late game cleaning and are forced to go to -2 to use your STAB attack. And if you use PsyShock as your STAB, you will have subpar coverage for that late game cleanup.
As for the other sets, they are not as threatening due to the fact that they take a turn to set up or lack power once they are set up.
Dragon Pulse / Surf / HP Fire / Calm Mind cannot nuke much of anything with the huge power difference between Dragon Pulse and Draco Meteor.
Draco Meteor / Surf / HP Fire / Recover lacks the power of Specs or CM in exchange for some increased longevity, yet it still loses a consistent STAB attack and no longer has room for Trick or Psyshock.
Running HP fire is worth it to get by several checks like Jirachi (weakened) Scizor (non-CB) Nattorei & Excavalier. Running HP fire isn't really a big penalty. Gengar is nowhere near dominant in this metagame, so getting outsped by him is no big deal. Sure you auto-lose to opposing Lati@s but its worth it. Also speed ties are dumb.
HP Fire is worth it, yes, but you need to predict perfectly (assuming Specs) to even catch them with the move, and it doesn't help it get by ALL of its checks. Being able to take out a weakened check is nothing special, either, and if you run into a rain team HP Fire is essentially useless. Specs Surf will fail to 2HKO SpD Jirachi and Ferrothorn, the most commonly seen steels on those teams. SpD Metagross and Escavalier can survive 2 Specs Surfs outside of rain, so Latios needs to be careful around them a well.
EDIT: The release of the third game may see Blaziken return from Ubers if the current DW tier is any indication. It has several additional checks in the form of Techniloom, Chandelure, Keldeo, and most importantly Imposter Ditto. Hopefully any movepool additions will help check it just enough to bring it back.