Kaspersky was likely targeted because they are very popular in that that part of the world: Russia, middle-east, so forth. Owning Kaspersky, if indeed it was a complete compromise, in effect means you can access data(potentially execute) from every single computer that runs Kaspersky software: you are in a position of trust at this point. Trust is a _dangerous_ thing in computer security terms, do not let this fool you. As most antivirus software will send home "suspecious" files for analysis, I expect they would leverage this functionality to have well hidden backdoor in legit, properly installed software. Of course, here is also the source code: bug hunting it much easier with it, hence why the only program with even a slight chance of being trustworthy is one you can get the source code to, given that someone with the proper skills audits it.
It's about high time we realize that closed source ecosystems is horrible for security; because it can be challenging to actually audit, or at least time consuming.
I wish hackers would stop selling script kiddie-ready 0days to governments, these people have no idea of the power they wield with these things. I'm looking at you the grugq, etc: you people are a disgrace to every hacker in the known universe and you are actively helping authoritarian regimes and agencies with no oversight to suppress people and other countries, and profiting off it.
In any event, I believe that the stuxnet team learned a lesson from their run of stuxnet in Iran; namely that there are easier targets to compromise to get in there with better access, because how do you beat the people you can't beat? you join them.