It's a sound theory, it just doesn't make sense to me that he'd allow a civil war because two teenagers might be better rulers than Tywin fucking lannister.
Were all the Targaryans Augustus Caesars and Queen Victorias with exception to the mad king?
I think it's Selmy that explains the madness took like, every other generation. The Mad King's grandfather (Jaerys or something?) was crazy as well but I think it was mitigated. There are *a lot* of stories about the targs though; many of them are venerated as being the best of the best - there are inns named after some when they came to visit that area on dragons etc. Not until the Mad King really started fucking specific people over was their villainy really shown.
I can buy the whole Varys wanting what is best for the realm. At least in the book, wacky things conspire to make sure a targaryen is alive and it turns out Varys had a part in it.
Also, of all the other people in the entire book, Varys needs nothing from anyone. He doesn't even need a companion because he's a eunuch. He needs no gold, or home, or food, because his power comes from secrets, and everyone has them. Other than losing his head, he can safely avert just about everything else, and stave off death by simply vanishing.
In talks with other characters, I think he subtlety gives the impression that he, above all others, understands that the true threat is elsewhere, and believes what he does to be for the good of all. The three targs he has saved so far have been groomed and trained to be rulers, knowing that they serve the kingdom. That is a comment Varys literally makes word for word - that all rulers serve, and they have to safeguard the realm. Viserys was an asshole but fortunately Drogo took care of him. The only thing that changes is that Varys will have to figure out how to get Dorne into the equation (which probably won't be hard since the Viper's death.)
Varys made a gamble, but an educated gamble, and now he has the perfect setup. Varys has never struck me as greedy, ambitious or anything else. Maybe I'm being gullible but I can honestly see him being altruistic.
Also, someone mentioned Tywin. Varys needed Tywin dead because he was fixing things in the empire. The blood feud between the current rulers and targs would have made it necessary to probably kill or at least fight Dany's army with the dragons that the realm so desperately needed. This is also the reason that Pycelle and Kevan end up dead later.