This is a great question!!!
Twilight Princess- Tear collecting...
Pretty much ALL JRPGs (that do it)- When/If your party gets split up... They never do it right, shit gets unbalanced, and it drags for too long.
Jak 2- Sewer escort *the horror*
Jak 3- Final boss made me go completely ballistic
Mario and Lugi Dream Team- *I haven't completed this game yet, but this has to get the slowest starting game ever... Tutorials out the wazoo, they give you a tutorial for EVERYTHING. How to save, how to use an item, etc..
Red Dead Redemption- Boat survival mission... I forget the mission, but you're stuck in a boat and everyone is shooting at you, took so long for me to beat it.
Spiderman for the PS1- There was this final section where you had to escape Monster Oc, gave me nightmares and I was too afraid to beat it, back when I was a kid.
Uncharted 1- Chapter 4 and Chapter 11... dragged for too long and was really challenging, really made me rage.
Halo 3- Cortana mission
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