The reason Shinsuke Nakamura has been main eventing dark matches is WWE’s attempt to keep fans around after SmackDown & 205 Live ends. It’s been well documented that fans have been leaving the arena after SmackDown Live ends and not staying around for 205 Live, which airs directly after SmackDown on the WWE Network.
In regards to Nakamura not competing on SmackDown yet, the belief is that WWE is saving Nakamura vs. Ziggler for the upcoming WWE Backlash event in Chicago. Nakamura will receive a great reaction at this event, much like the reaction he got in Orlando during WrestleMania week.