I am Naut Main and I have like 1800+ games with thim.
Reasons:
-E nerf made a huge difference in damagewise. So to cover that you need to build Runic Echoes and if you do that you lose early tankiness and whole point of Naut was being early tanky yet he could deal dmg.
-Shield nerf is a minor change but with the adc and mage patch they already got big fat items which has armor /mr penetration. So sustain is gone too...
-Earlier (Before dumbs on LCS decide to play Naut on Top lane) he was not getting picked alot so people didnt know his passive (which is the biggest reason ppl lose teamfights) Now all ppl know his skills and capabilities.
-REaching the damage dealing Tank Naut before patch is possible with item build but it is the most expensive build.

-Naut is team relient. If you use your cooldowns you need to wait for tons of times. If you teammates cant use that opportunity you are giving them you basicly lose teamfights.
-Naut is a late game TEam comp champion. After Mage and ADC update games end in 20-30 min mark.
These are the reasons imo.