I don't believe there is any lore connection between the flamewakers and the naga. It's like you said: They just happen to share a skeletal structure in the game. The naga were elves transformed by the Old Gods' influence. The flamewakers are fire elementals, but they are unique in that they are flesh and blood elementals. Flamewakers are native to the elemental planes.
It's possible the Old Gods transformed the naga in the flamewakers' image, but since both creatures have roots in real-life mythology, they were probably added to the Warcraft universe independently. The naga are based on Earth's nāga, and the flamewakers are based on salamanders.
Why did Arthas never bother making any more of the original style deathknights? They seem to be more powerful than the kind he was been making and I assume there's some more Orcish necromancers about, with some of them even working for him. And it's not as if it's hard to make more dead human knights. I mean, he did make himself so I'd assume he knows how. So why bother with all these guys who couldn't even clear Stratholme?
Ner'zhul doesn't necessarily know how to create that brand of death knight -- or if he did at one time, he may not anymore since becoming the Lich King. It's also possible the old orcish brand of death knight isn't actually any better than what the Scourge can make from an in-world perspective. Teron Gorefiend was pretty bad ass, but we killed him just the same as Deathbringer Saurfang. Ultimately, it didn't matter a whole lot.
Is there some new mechanic for the random dungeons that pairs specific DPS together? I've noticed that it never seemed to put two of the same class/role in the same group, but this week for every random I did on my hunter there was always a warlock and rogue for the other dps slots. Even if one dropped/was kicked, they'd be replaced by that same class.
The dungeon finder tries to avoid putting classes that share armor types together. It won't always succeed, but ideally, you won't end up with multiple cloth DPSers or multiple plate DPSers and so on. It tries to ensure as little loot competition as possible, to maximize everybody's potential rewards.
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