Good to know I'm not alone. I've been trying to update the Splatoon US version and so far no success. I have tried faster SD cards (Class 10), waiting longer (10 hours just this last try), and I still get the "Unnecessary Data" error after restart. However, I was successful in updating Super Mario Maker, so it still works for at least some things. So far my results have been:
Successful:
1. 5.5.1 version title spoof (installed easily)
2. Super Mario Maker (newest as of 1/13/2016 - Class 4 SD card, waited about 1.5 hours for 189MB update to install - able to go online/download courses, etc. and update shows up properly in data management).
Unsuccessful:
1. Splatoon (newest as of 1/13/2016 - Class 4/10 SD cards tried, waited 3/5/10 hours for 579MB update to install - so far "Unnecessary Data" message every time).
2 things that were different between these games before trying to update:
1. Super Mario Maker had NEVER been updated before, so there wasn't an existing update that needed to be changed/removed
2. First attempt that did anything for Splatoon, since it had been updated before, left a corrupted Splatoon update showing in data management with an "!" over it. All I could try to do was delete the update and try installing from scratch, which ever since has left the game unlaunchable (it was also unlaunchable with the corrupted "!" update) and every attempt has resulted in "Unecessary Data".
There must be something different about this update in terms of size/etc. that is making it fail since multiple people are experiencing problems with installing it. Has anyone been able to successfully install any game updates on 5.4.0 BESIDES Super Mario Maker/5.5.1 spoof? I would be curious to know if anyone else has had success and with what games/sizes of updates/how long they waited for it to install/speed of their SD card. (I'm also wary to try updating any other games as I do not want to render them unplayable like Splatoon currently is...)