Linear games like Uncharted aren't bad, but  linearity can screw up franchises which are known for being nonlinear ( Metroid being a good example of that with Other M).

No, Jump 'n' Runs and games like Uncharted are awesome!

That depends. I don't mind linear games, but games that give the illusion of being open, but has invisible walls everywhere is just annoying...

Linear games are fine, but when they are too linear (ie: cramped/corridor shooters) it leads to repetition and boredom.

Linearity is better imo.  With linearity, players are confined to do or progress the way developers want you to.  Even if a game is open world, a good mission usually forces the player through linear sections of a game to give them an experience in level design the developers intended.

In Infamous Second Son there were too many main missions that had you dashing across the top of uildings going from checkpoint to checkpoint.  Rather aimless in level design.  In the first Infamous you were led through certain areas and you'd always get the same focused mission each time you play.