Finales are difficult.
If it’s a season finale, the writers need to tie up loose ends, but open up enough cliffhangers to make you want to come back for another season.
It it’s a series finale, they usually want to provide people some closure, or confuse people enough to make them hate the show and watch again (because we as humans enjoy that punishment).
Sometimes writers have the luxury of knowing that their shows are coming to an end, and have plenty of time to make everything fit neatly into the box (ex. Friends), while other times it is told to them after the (now) last season has already wrapped up (ex. Nashville).
But often times the writers know before we the public find out, and are able to gear the show in the right direction.
Two shows from this year that are good examples: Person of Interest and Nashville.
Person of Interest knew that they were getting a half a season in 2016, and that it would be their final one. As such, most of this year has the feel of ‘wrapping up’, and I like that, and hope that it finishes in a satisfying way.
Nashville had rumors all year of it coming to a close, but it wasn’t decided until after the show had finished taping that it wasn’t going to be returning.
As such, the “series finale” was treated like a “season finale”, but the feel of the episode was “The Writers Knew”. <No Spoilers> Wrapping up some storylines, tidying up relationships in one way or another, and lastly finishing with a big bang, that if it is indeed the series finale leaves enough to the mind that I am satisfied with it.
If they didn’t know OR if it does get renewed at some point, there is so much there to build off of.
Aviously 
The writers of Chuck seemed to think every season after the first (and sometimes even half seasons, as they initially only had an order of 13 episodes before it was upped) would be their last, so it has like 5 ‘series finales.’ I think that’s the safest way to play it.