I thought that might happen, so I figured that I would stick with the 2nd one and try to plow through it avoiding as much content as I could. I thought you should be able to skip the strongholds--territory capture that weren't actual game missions--but that wasn't possible.
I don't like that you have to capture every single piece of territory to unlock all the missions, but I guess that is the primary goal in the story. ...I actually just watched the final two missions on Youtube because I was tired of playing it.
problem I am having with SR3 is that with all of the DLC available the first time I play it, I feel that I am way too overpowered, wealthy, with great property and vehicles, weapons that are insane, unlocked abilities. ...however, these gang activity missions can still be quite difficult because they will spawn backup very quickly, and things get hairy.
I'm also trying to avoid the DLC missions, as I started one of them and it makes no sense--figured it was DLC.