That was the big problem in this matter.
Just like you, several got tired of the treatment that Natsu receives from Mashima, not giving him a better development, always making him look like a fool who doesn't think and doesn't know several things, we know that part of Natsu's character is to be funny and his great charisma, but Mashima goes overboard with the comedy in character.
In the most recent podcast that Mashima made on his Twitter, he said that he forgets what happens on FT, for the same reason I think that Mashima forgot that he gave Natsu very good moments in this sequel (in the fight against Aldoron and the sky beta thing for example).
Natsu is one of my favorite characters in the series, but I feel that Mashima doesn't give him the seriousness at the right time, in fights he generally makes him look much more mature and intelligent than in other situations, but that's it.
And no less important, I was really sorry to see how Mashima wasted the whole E.N.D. thing, I'm not a Mangaka or anything, but I humbly think that this situation would have been used much better for Natsu's own growth and in this sequel for the confrontation against ignia.
Anyway, we are only in the middle of the sequel according to Mashima, I still have some hope for the author to give his MC a good growth and a good conclusion.