I think part of the problem is that the RTS features these characters, so even when it kills a few (like Terenas Menethil) it offers up a few more. But the MMO features us, ultimately, so when we put down Lady Vashj or Arthas, there's no immediate replacement. To be sure, there have in fact been tons of new faces over the course of World of Warcraft - Ragnaros, C'thun, Nefarian were all first introduced in classic WoW, not the RTS. The problem is, we introduce these characters and then, well, we dispatch them. Sometimes, like Ragnaros, our first encounter with them isn't a final one, but even if we know they'll eventually be back, it's not like their luck will hold out forever. I called this the "Joker problem" once, and to a degree I think it is an issue for the MMO.
However, does it follow that we need an RTS to create stories? Since I think Mists of Pandaria did an amazing job of building up the story, and in fact I'm really much more of a Cataclysm booster than most, I don't agree with that idea. In fact, in many ways, WoW has done more to broaden and expand the Warcraft setting than the RTS ever did.
- The Ethereals.
- The Naaru.
- Elemental lords
- Argus, Xoroth and other worlds
Note that this doesn't mean I think they shouldn't do another RTS - in fact, entirely the opposite. I do believe a Warcraft IV could be an amazing, story rich game. But frankly, it will benefit from the lore expansion made for the MMO as much as it could possibly bring any story benefit to said game. Characters like Varok Saurfang, Bolvar Fordragon, Varian Wrynn and Garrosh Hellscream who either first appeared or had the majority of their stories told in the MMO would add to the fertile ground for an RTS. The expanded world of the MMO would create whole new places for an RTS to explore - imagine a world campaign that takes you from Northrend to Pandaria to Deepholm? That let you play as a new Vrykul character seeking to unify her people and conquer Azeroth?
Honestly, the problem with comparing the RTS series to the MMO is, the RTS storylines had an entirely different ability to simply go off in new directions because nothing was established yet. Each iteration of the RTS completely expands the setting - broadening outwards from a small kingdom under siege, to a continent in conflict, to an alien world and finally revealing Kalimdor and Northrend, always expanding. Meanwhile, the MMO started off with the goad of fleshing it all out, giving you a chance to visit these places. But in its continuous years of operation, it's finally started to go beyond the fleshing out process - Cataclysm was the point where World of Warcraft said "Now, let's start looking for new places" and Mists of Pandaria was the first such place given to us to explore. I think Mists has proven that the MMO absolutely can handle any storytelling you need, as long as you're open to the basic premise instead of just sating "Pff, pandas are dumb" and walking away. In this one expansion we've gotten ancient Titan fortresses, the mantid (an entirely new kind of threat in that they're rational worshippers of the Old Gods), the Isle of Thunder, the Timeless Isle, and several key points in the history of the Alliance/Horde conflict.
If anything, Mists of Pandaria has been so full of story that it can be overwhelming to try and list it all.
If anything, this all means that when a new RTS comes out, it will be the game that ends up stealing story elements from WoW as much as the other way around, and it will be the better for it. That being said, though, the other point stands - WoW does blaze through its villains and lore figures at times. Recent developments of a spoiler heavy nature have made me a little happy to consider the future of the game, but we won't discuss them here. It would be good for WoW and the setting as a whole if we had a few more Darkseids or Doctor Dooms, guys who just keep coming back over and over again. I have hopes for Azshara in this regard.