Registeel with Thunder Wave and/or Ice Punch usually beats Salamence and Latias. If you play UU, you probably have an idea of what this thing can survive. The fact that it has an Ubers moveset listed speaks for itself. Back it up with Wish, though.
It doesn't counter New MixMence at all. Fire Blast is doing at least 62.6%, which is quite a lot! It counters Latias fine though. If by "beat" you meant Salamence can't switch in, well you could say that about a lot of pokemon (Jirachi, Scizor, Heatran). Regardless, I agree it is a good wall and should be used in OU more.
Regarding your Uber point: Shiftry has a set in Ubers. Registeel simply fills a niche with its steel typing and high defenses.
If you can consistently keep Stealth Rock away, Moltres is an even better counter to Scizor and Metagross than Zapdos is. It's pretty good at SubRoosting against other kinds of opponents, especially with Toxic Spikes out. Seriously though, keep those rocks away or this shouldn't be bothered with, I admit it. In one of Obi's RMT's, he states that one slot of his team was a toss-up between Zapdos and Moltres.
Yeah, it is a pretty good pokemon. Like you said though, it's has that horrible weakness to Stealth Rock. For this reason, pokemon like Zapdos and Rotom-A remain better counters. It's not easy to Rapid Spin on an offensive team without Starmie, and players don't want to dedicate an entire spot on their team for supporting Moltres. Even if the team is based around Moltres, it's still a stretch to do that.
Most bulky Poison Pokemon can counter Lucario, especially Weezing. Nidoqueen even has Roar, Toxic Spikes, and Stealth Rock among her wide list of other moves, and could potentially even fit on a stall team despite only OK defenses.
http://www.smogon.com/forums/showthread.php?t=45814
This is Jabba's team in which he used Nidoqueen. It got into the archive, showing that Nidoqueen must be able to function pretty well. I'll comment on Weezing later in this post.
One my favorites, though I haven't used it in ages: Regirock can lure and beat Infernape, Lucario, Gyarados, Heatran, Salamence, and even Gyarados 1-on-1. I stopped using it because of things like Breloom, Machamp, Hippowdon, and Swampert, but still... With Fire Punch and some speed investment, you can also lure and kill Scizor. And I haven't even mentioned Wish or Dual Screen support yet...
I'm curious... How does Regirock lure in those pokemon? Players aren't stupid, they know it'll be carrying some rock move. I have no idea who would switch in a flying type like Gyarados or Salamence. If I saw a Regirock, I'd also assume it was carrying Earthquake, and switch in those other pokemon (also, why would Heatran
ever switch in to Regirock. If you're using Regirock, you should also be using Sandstorm. Heatran can't touch Regirock. Choice Specs Earth Power barely manages to do over 50%, the strongest attack it can use.). I do understand Scizor though. I would never assume Regirock is using Fire Punch, and try to get a free U-turn/Bullet Punch.
Slowbro, Dusknoir, and Spiritomb are pretty much the only true counters to Machamp because they wall and avoid confusion from Dynamicpunch and can also take Payback well (Slowbro and Dusknoir are slower and get hit for half power, Spiritomb isn't Dark-weak). Slowbro can spread Paralysis with Thunder Wave or attempt a Calm Mind run. though Scizor will usually rain on its parade with U-turn. So, you'll want a Magnezone or something if you want to try that...
Spiritomb can fill niches on stall teams - spin-blocker that doesn't get completely destroyed by Tyranitar. I beg to differ about Dusknoir beating Machamp. Once you realize it can't kill you with an unboosted Payback, you then soon realize that you can't do anything back if Machamp can heal. Slowbro also completely stops Gyarados, but the weakness to to Scizor's U-turn hurts its walling potential a lot.
And two offensive threats, since I might as well do the whole package...
Mismagius may not be as fast or powerful as Gengar as far as base stats go, but she has Calm Mind, Nasty Plot, and the special defense to survive the setup. She completely owns Blissey with SubCM just like with Chansey in UU, and hits Tyranitar 4x effective with the Hidden Power Fighting she already carries. Scizor is still an issue.
Actually she can't beat Blissey at all. 32% - 37.8% is how much Missy does at +6 with HP Fighting to standard WishBliss. I don't really agree at all with HP Fighting. Even at +1, Missy can't OHKO CB Tyranitar with HP Fighting. Besides that, Gengar can also use HP Fighting, you make it sound like it's an exclusive move to Missy. However, Gengar prefers to use Focus Blast in hope of an actual chance to OHKO Tyranitar.
Raikou is stronger and bulkier than Jolteon and still blindingly fast, and its Calm Mind + Life Orb set can really tear many Blissey-less teams a new one while not taking much from Scizor's Bullet Punch or even Lucario's Extremespeed. Only the lack of Volt Absorb and inability to outspeed +1 Adamant Gyarados make Jolteon the more popular choice.
Yeah. I seriously do not know why people use Jolteon over Raikou. Unless your team is really weak to Gyrados, or doesn't have an electric immunity (I will say though that this is very useful - offense teams suck if they get paralyzed), Raikou will almost always be the superior option for sweeping. The speed doesn't mean that much. You lose the ability to definitely beat Starmie, and outspeeding Gyarados and Scarf'd Heatran. Heatran and Starmie aren't big deals - remember, you have a Calm Mind (or at least you should). Earth Power from Heatran seriously does under 50% max. I already adressed Gyarados.
I already stated that some of these pokemon could be useful, but other ones not so much. Other pokemon just do these things better. Not in the normal way, like Rotom-H can counter Lucario better than Weezing. It can't. However, Rotom-H also checks and counters other stuff that Weezing can't, making it be more greatly considered for spot on your team. This is a problem that some pokemon face - they can fill a niche, but it's not a very general niche. It can't counter only the top sweepers, it can only counter one or two of them. Unless your team really needs them, it's probably best to stay away from them. Some of the pokemon you suggested (like Raikou and Spiritomb) though I have to say that they are viable in OU.
About Uber Borderline - actually, the name doesn't make sense. Uber pokemon are broken in OU, much the same like Borderline pokemon are broken in UU. I don't know, I guess it could be called like "Uber Used" or something. But anyway, I don't really get the point of banning overused pokemon. Of course if you ban the top six pokemon it's gonna effect the metagame, but no necessarily in a good way. People will take a while to adapt to the new game, and by the time they do the old pokemon will be unbanned and new pokemon will be banned. This basically creates a fast changing metagame, but in a way like if they suddenly banned the top tier characters on Brawl. People will use new stuff, but once the metagame goes back, the creativeness will be gone because the creative pokemon are now banned! It just doesn't make sense to me.