In investigating a Week 17 versus Week 16 Championship, the pros and cons were evident, it was something I investigated heavily.
On the one hand, you can have some of your best players sitting out the final week, in fact, my top pick is sitting on the bench this week.
But I don't really think this is a bad thing.
Fantasy is too often decided by a preseason draft that decides the winning versus losing teams, to where the weaker teams can't right the ship through picking up players because one team out of twelve through luck of the draft is going to be fill a team with stud players that remain healthy.
To me, fantasy is about more than that, its about paying attention to your team and other players and being a grind. Having a Week 17 Championship allows for this - deeper teams mattering, the draft being important - but not everything, and ending this final week on the last week of the regular NFL season. You've got six bench slots, if you have a player or two sitting out and you haven't picked up anyone to fill the gap in the playoffs then that's on the manager, and a playoff manager at that.
You'll have a good idea if one of your starters is sitting on the final few weeks of the season. It makes the league tougher, but it also brings more meaning to Fantasy football, where the bench is often an afterthought for plugging players in for starters during bye weeks or when they get injured. That's why people don't really do 4, 6, 8 team leagues, because you'll never really go to the bench, and the leagues are termed as "easy." Opening up the bench to matter is what makes fantasy better, exciting, and also more of a challenge.
For most teams, playoff weeks in 16 and 17, won't matter because they won't be playing anyway, but if you've managed to make it that far, then the championship should be fought between the two managers. The draft will still matter because the majority of your players will still be playing, but it also opens the bench up more so it isn't plugging most of the same players in since day one.