Having played every single FC game, I think FC5 was the worst in the series. It's so bland and loses everything that made the series fun, including exotic locale.
I think Blood Dragon is the best overall, and FC4 is the next best for gameplay. FC3 is great, but people overrate it and either didn't play it or don't remember it. Vaas isn't even the main boss. He's a sub-boss and you literally only see him like 3 times. I think Hurk has more development than Vaas.
FC2 is an underrated gem I wish people would have patience for, cause for all it's frustrations and faults, no other FC is what FC2 was trying to be, and it's such a unique experience.
The original premise was "you set out to accomplish something and everything keeps going wrong." FC2 does this better than any of the others.
My biggest consistent gripe with the series is the lack of main boss development. They tease the shit out of the main enemy every time, but it winds up being barely a part of the story. I wish there was more character development and buildup to the end. But ultimately, FC is about the gameplay, kind of like Just Cause. We're hardly there for the story.
Also FC6 was excellent and a massive improvement in fun over FC5. I don't care what most people say.
FC1 campaign was not fun, but building and sharing custom maps on Instincts Predator on Xbox 360 back then was so much fun.
Ah yes, the buddy thing was pretty neat, and in some ways your choices even from your starting character had some meaning. They could have done so much more with that by now.