Note: Though everything is based of known lore, there is a lot of speculation done in this post. Don't take it all as fact.
Dave Kosak mentioned in the Jesse Cox interview that we know of the origins of the Old Gods, and that the info we have is meant to be contradictory, but does point to a final conclusion. I immediately started thinking of where Old Gods could be from. It reminded me of another interview he did in which he mentioned the Titan's killed many Old Gods. This goes against the 3-5 we've been told existing. Then I started thinking of things like http://wowpedia.org/Iso'rath, and what exactly they were. That's when the speculation began.
Origins
The Old Gods have been called outside the cycle. They cannot be killed in the usual sense, as shown in Y'Shaarj, who is still essentially alive. It was confirmed (http://us.battle.net/wow/en/forum/to...94?page=13#260), that the only way to kill an Old God would be to somehow erase it from existence. That means only one thing to me, the Old Gods do not reside in the normal realm.
This is where I get crazy. Opposite to the Naaru, who I believe come from a separate realm of 'Light', the Old Gods are from a realm of 'Chaos'. This is why the Old Gods thrive in it, and there number one desire to bring the world to it. Old Gods do not fly to a planet or arrive there. They simply appear; Manifest.
Iso'rath, and the other's like him in Dragon Soul, (also other minions like http://wowpedia.org/Soggoth_the_Slitherer), are Old Gods. The thing is, they were defeated and/or imprisoned before they had the chance to manifest on Azeroth completely. The more an Old God manifest, the more ingrained with the planet it becomes, the more powerful it is. Old Gods like Y'Shaarj, C'thun, Yogg-Saron, and most notably N'Zoth, are all heavily if not completely ingrained with the planet, hence there power and influence.
War with the Titans
The Old Gods were on Azeroth first. I base this off the existence of http://wowpedia.org/Contents_of_Mosh%27Ogg_Bounty, which is believed to be 150,000 years old, the oldest known date in WoW, and is believed to be from an Old God. Sargeras turning the Eredar was a priority after becoming a demon. He did this 25,000 years ago.
I don't know if it has been confirmed Sargeras never stepped foot on Azeroth, but I doubt he spent over 125,000 years searching for the Eredar, which he would have had to if he was on Azeroth with the Pantheon, fighting the Old Gods.
Anyways, here's how I believed it happened. The Titans arrived at Azeroth during the time of the Old Gods reign. They thought nothing of the Old Gods and there minions, who they simply believed to be mortal monstrosities. They defeated and killed many of them (obviously, the lesser Old Gods such as Iso'rath and Soggoth), and seeing a large number of them gone set out on fixing the planet. They made their constructs and complexes, and began shaping the land. This is when they realized they made a vital mistaken in how they dealt with the Old Gods.
There constructs were becoming fleshy, the 'monsters' seemed to be returning, and the Elements began taking shape and attacking the Titans. This began the war of the Titans and the Old Gods, where the Titans realized killing the big ones had horrible consequences. It was after defeating and imprisoning the Old Gods and their Elemental Lords, that the Titans created Azeroth as we know it (sorta). They let certain races (Earthen) live free, and others like Troggs get imprisoned.
The Mogu and Vykrul turned fleshy and mortal AFTER the titans left. I have a feeling that what they refer to as Gods more than often enough is the Titan Watchers, more specifically Ra'den for the Mogu and Thorim for the Vykrul.
Anyways, thoughts?