I feel that the series has always had some mix of serious drama and light comical fun and I don't feel MGS3 was more either way. Of anything I think your sense of humor is just different from the design team's (nothing wrong with that btw ).

The arm breaking thing is quite absurd but remember we are playing a game so some liberties have to be taken. I actually liked the ladder scene and only found it comical when it was later satired by VG Cats and other fans of the series but during the actual game I found it no different from musical interlude's used to create tension or other feelings. I didn't find the bosses any weirder than previous installments. Of anything I was happy to face a colorful cast of villains instead of the lame ones' in MGS2. Besides, have you ever seen the villains from the MG series for MSX? Running Man? Shotgun Joe? Arnold(actually made to be a rip off of the T-800 of Terminator fame)? The series has a long history of goofs and TV movie rip-offs. Its what makes it so damn endearing.

The series is canon as it basically tells the story of the origin of Big Boss and his reasoning for creating Outer Heaven and betraying his country; as well as the origin of the Patriots as you mentioned. Considering how pivitol of a character Big Boss is to the series I highly doubt it could ever be considered non-canon cause its theme song is a James Bond-spoof and the bosses blow up when they die. To this day, only Snake's Revenge, Ghost Babel, the Ac!d series, and the radio drama's are considered non-canon in the MGS timeline.