The one thing I will blame Iwata for is under his leadership Nintendo has failed to create (or really even try all that hard) any new long lasting I.P.
The whole Brain Training/Nintendogs/Wii Fit/Wii Sports crazes were immensely profitable for Nintendo, but really, these franchises have burnt out and had their moment in the sun.
Nintendo failed to properly invest in making new franchises and cut off most ties with Western 2nd parties (bye bye to things like Perfect Dark, Conker, Killer Instinct, Eternal Darkness, NBA Courtside, Star Wars Rogue Squadron, etc.). At NST things like Project: HAMMER were canned.
Nintendo's answer under Iwata to everything nowadays seems to be "just throw Mario at the problem". 3DS in trouble? Throw Mario at it (Mario 3DL + Mario Kart 7). Need to maintain 3DS momentum? More Mario (NSMB2 + Paper Mario). Need to launch the Wii U? More Mario (NSMB U).
They're like a coach that is wearing out their star player by failing to develop any other talent.
Under Iwata, Nintendo has not had a hit new character-based I.P. franchise in 10+ years. The last one Nintendo really even tried with was Pikmin, and that was a moderate success.
