I don't get the feeling that the plans for Ulduar were changed. At least, not since the development of the Storm Peaks (but perhaps after the development of Howling Fjord). Everything about the way the instance is set up heavily suggests that Yog Saron was always intended to be there. The corrupted watchers who help you fight later in the instance, large portions of the instance's art and design, and the not thrown-together-last-minute trailer are all obviously designed with Yog Saron in mind. I don't think vague references to "Father" really have to be someone aside from Yog, especially because we already know that Yog Saron is really big on pretending to be someone else in order to manipulate people. Also, in the quest in Storm Peaks where Thorim is taken (the culmination of a quest-line that is a huge part of the structure of the zone), it is obviously done by a shadowy tentacle. The fact that most signs in many of the quests pointed to Yog Saron being deep in Azjol-Nerub may have meant that we would've ended up finding out his true location in the Azjol-Nerub zone quests. Perhaps the ultimate quest-line in the zone would've ended with us forcing Yog Saron to retreat back into his former prison, who knows? The only thing I really buy as a change to the ultimate Ulduar plan is the possibility that Tyr was removed.

Also, I don't think Sara was ever intended for anything but exactly what she's used for. The whole concept is very simple, it's a damsel in distress and your raid is trying to save her throughout the instance. You assume she's a good guy because she's fighting the bad guys, and she's a vrykul because it makes sense for there to be a vrykul in Northrend and they're faction neutral. Could Blizzard have done something to more involve you in having a reason to rescue her? Sure. It doesn't mean that because they didn't that there was some huge plan they wanted to implement but never could.

EDIT:
Though, now that I think about it, it is entirely possible that she would be a character you interacted with in the Azjol-Nerub zone. In fact, I think that would've made a lot of sense, if many of the quests that you did in there involved her.

Some added thoughts to the whole Sara thing I came up with reading stuff:

I do get the feeling seeing some things that she was initially intended to be a more elaborate double cross, in the tradition of Drakuru and Loken. Just looking at her, the buffs she casts are double sided in phase one, she is neutral, and then during the phase transition the voice gradually changing to Yogg's and her becoming hostile. While I know most players would have guessed anyways, last boss incoming and all, I'd say that in a lore kind of situation she was intended to double cross the players. The problem with this is that in the current situation there is no meaningful double cross, since we have this "Who is this Sara and what is she doing here" feeling due to no prior introduction. (Aside from pissing off raids by yelling at the most irritating moments)

Basically the Vrykul subtype Sara seems to be of model wise is the 'regular' Vrykul (for lack of any better term), which are pretty much entirely Scourge alligned so not likely to be considered friendly to player races. The only Vrykul subtype which shows some sort of dedication to good (to Thorim), is the Hyldnir in the Storm Peaks, though in a rather harsh and not entirely agreeable way.


Overall I don't entirely agree with Ulduar being a smooth experience. A lot of it makes sense (The Siege, Veranus turned Razorscale and such) ties in flawlessly with the outside of the Storm Peaks. The Keepers make a lot of sense in that it was clear they would be corrupted by whatever entity was behind the mess in Ulduar. Beyond this though, there's some issues:
-Kologarn and Auriaya are essentially loreless bosses of which each instance seems to have a few. Not much to say, visually they fit in but they do nothing to add to it but being a bigger named mob dropping epics and being part of achievements.
-While the previous part of the instance could easily have been fine with any master in Ulduar who was up to no good, the Descent into Madness marks a sudden shift into things indisputably alligned with the Old Gods, with Vezax' and YS' presence. Nothing wrong with this, but the whole situation does not eliminate the option of the remainder of the instance with the Descent into Madness fitted in after YS got moved at some point during beta.
-I just feel there's a huge amount of loose ends with the Iron Dwarfs/Giants/Vrykul. They feature prominently from Howling Fjord to Grizzly Hills and then Storm Peaks and the pre-Descent parts of Ulduar. However they are never entirely explained in terms of origin, there is no background behind the Iron Council for example. Overall the whole Dark Runed 'race' is one major loose thread of which little is explained beyond that they are somehow created in Ulduar, looking at Halls of Stone. It just makes me wonder if originally a master of Ulduar was intended who was more linked and similar in nature to these beings ('Father' ! ), rather than Yogg-Saron. (for whom they are useful roadblocks but bear next to no link to him - even if it could be a case of using the materials at hand)

I realize it's all speculation, and I don't think we will ever find out unless someone from Blizzard comes out or we see older development documents or so. Part of it might just be that Blizzard storytelling while usually good doesn't always live up to the potential we see as community, and tends to leave high amounts of loose threads which are never revisited. But it does have me wonder.

I think mimiron always thinks in those terms. I think they were all created with a prime directive but they're independant beyond that.

My concern is that it's not going to be so cut and dry. In Naxxramas 1.0, we down Kel'thuzad, but delivered his phylactery to Inigo Montoy, which sets up Naxxramas 2.0 (kinda). In AQ40, we down C'Thun, but even then it's not certain that C'Thun is inactive or that the Qiraji are gone for good. In Sunwell Plateau, we shut down Kael'thas' gamble to bring Kil'Jaeden into the show, but he's neither dead nor really defeated, and neither is the Legion. With a force as powerful as Arthas and the Scourge, I get the sense that while we might defeat Arthas himself, the Scourge might remain a threat. Diminished, and perhaps lacking the unifying will of the Lich King, but still a threat.

Meanwhile, on the list of threats that were pretty officially shut down: yes, we did kill Thaurissan in Blackrock Depths and that shut up the Dark Irons. We killed Rend Blackhand in UBRS and that shut down the Old Horde. Nefarian and Onyxia are dead, though Big Poppa Deathwing is still hanging back as a looming threat. And we did officially shut down Hakkar pretty effectively. And while they somehow keep coming up with more crazed fanatics to throw at us, I'm pretty sure the Scarlets are gone for good.