Pikmin 3 had a dedicated director and producer, both not named Miyamoto, who took the lead roles on the last 3 Pikmin releases. I think they deserve the credit.
When people want to validate Miyamoto's job, it should be based on how the EAD Division has been growing and adapting to the newer cycles of development. Which definitely has room for improvement. The man is a Board of Director and GM. Process how much time he has even on the games "he spent a little more time on".
There were two directors for Pikmin 3:
1) Shigefumi Hino, who has been a co-director on every Pikmin game
2) Yuji Kando, who was a core game systems programmer on Pikmin 1 and 2
Hino was the driving force of Pikmin 3...Kando was more in charge of the programming, but both worked together to make Pikmin 3 great.
Miyamoto was involved in the project from the beginning, but you're absolutely right...he's a general supervisor that has Board and GM duties, and the creations that come out of Nintendo should really be attributed to the people who worked the hardest on them.
But Miyamoto can only name four off the top of his head that he does not oversee to make sure they retain that Nintendo quality?
Poor Sakurai, not even mentioned in the same breath as "Rehash Animal Crossing Guy" or "Another Mario Kart Guy."
I bet the people Miyamoto mentioned as his "star apprentices" are the people that he has the closest relationships to.
It's interesting that he doesn't mention any of Nintendo's current dominant game directors...you know...the creative driving force for the titles.
All of those people he mentioned are fantastic producers, and in the past they were great video game directors, but they are a step removed from the day-to-day production of the titles (some producers are more involved than others, of course).
Here are two very talented director powerhouses within the Nintendo umbrella that are worth mentioning:
Masahiro Sakurai:
Kirby's Dream Land (1992) — Director, Game Designer
Kirby's Adventure (1993) — Director, Game Designer
Kirby Super Star (1996) — Director
Super Smash Bros. (1999) — Director
Super Smash Bros. Melee (2001) — Director
Kirby: Nightmare in Dream Land (2002) — Director
Kirby Air Ride (2003) — Director
Meteos (2005) — Game Designer
Kouchuu Ouja: MushiKing -- Greatest Champion e no Michi (2005) — Game Designer
Super Smash Bros. Brawl (2008) — Director, Scenario Writer, Voice Actor
Kid Icarus: Uprising (2012) — Director, Scenario Writer
Super Smash Bros. for Nintendo 3DS and Wii U (2014) — Director
Junichi Masuda:
Pokemon Red / Blue / Yellow (1996-1998) — Programmer, Music + Sound Effects Composer
Pokemon Gold / Silver / Crystal (1999-2001) — Assistant Director, Game Designer, Music + Sound Effects Composer
Pokemon Ruby / Sapphire (2002) — Director, Game Designer, Scenario Writer, Music Composer
Pokemon FireRed / LeafGreen (2004) — Director, Game Designer, Music Composer
Pokemon Emerald (2004) — Supervising Director, Game Designer, Scenario Writer, Music Composer
Pokemon Diamond / Pearl (2006) — Director, Music Composer
Pokemon Platinum (2008) — Producer, Music Composer
Pokemon HeartGold / SoulSilver (2009) — Producer, Music Composer
Pokemon Black / White (2010) — Director, Producer, Music Composer
Pokemon Black 2 / White 2 (2012) — Producer, Music Composer
Pokemon X / Y (2013) — Director, possibly Music Composer