If there's a Pikmin 4 in development it's going to be an NX game running on Pikmin 3's engine. Even if this game was the Pikmin game Miyamoto was talking about, that doesn't mean they're not working on a traditional Pikmin 4 for the NX. It's not like it's a new thing for Nintendo to work on 2 different types of games for one franchise at the same time.
It would be one thing if this was a Nintendo Direct that had both 3DS and NX games being shown, but Nintendo hasn't even shown the NX in anyway yet so it's pointless for anyone to worry this means we wont get a real Pikmin. For all we know Pikmin 4 could be an NX launch title that will be one of the first NX exclusive games they show at the big reveal event in the near future. Until the NX is finally shown though, we just don't know.