Since the Morag Tong mostly operates in Morrowind, I wouldn't be surprised if they're no longer around after that province went the way of Fallout on us, but maybe they could have migrated along with the Dunmer refugees that left in time to avoid that fate, in which case, I suppose they could have set up business in another province, in which case, I suppose it's not entirely impossible that they'll appear in Skyrim, possibly presenting a rival faction to the Dark Brotherhood, but I wouldn't count on it. And even if they do appear in some form, they may not be able to operate as they did in Morrowind, because the Morag Tong, as seen in Morrowind, was also a product of the local society and culture, if they set up shop in Skyrim, they'd likely have to change their ways somewhat to fit in, if their business could catch on as well. After all, since the Dark Brotherhood is pretty wide spread, I'd imagine they're in Skyrim, too, and I doubt they'd take kindly to their ancient enemies trying to steal their business.
I agree with you, and I didn't like the Morag Tong because their legally sanctioned activities meant that they didn't need to be an undercover assassination group. They wandered into places, did the business, and pvssyd with the guards. There's got to be a more interesting way to kill people.
And this is why I preferred Oblivion's Dark Brotherhood to Morrowind's Morag Tong, the killings seemed much more interesting, because you were actually expected to use stealth, and if you wanted to get the best rewards, you often had to kill people in a creative fashion. With the Morag Tong, it was just walk up to your target, kill him, then show a guard you're writ and there would be no trouble.