I don't think he has any control over any of his ideas anymore, except for Pikmin.
How does one manage to not have control over one's own ideas?
Just to provide some examples,
Eiji Aonuma is currently in charge of producing all the Legend of Zelda games. Miyamato created the IP, but Nintendo owns it. Aonuma may ask Miyamoto for ideas, but ultimately, it is between Aonuma and the executives of the company as to what ideas are implemented.
Takashi Tezuka is currently in charge of the Mario series. Again, it's an IP Miyamoto created, but no longer works on (hence, he is given status as an "Executive Producer", which is often reserved for the lead producer and people who created the series but not the game). Tezuka is not a fan of SMB2 (USA), so odds are there won't be another one.
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