Native Son is a great song but lacks critical elements found in Vertigo.
The chords and structure of the of song stays true to Vertigo. The noticable differences are in the verse.
Intro: Gone is the count-in. It is replaced by an erry sounding guitar. As the main riff starts up, it is noticable that another guitar is present in the Native Son version. There is an extra lead guitar playing over the main riff. This continues in the post-chorus parts as well.
Verse: Native Son has a melodic verse while Vertigo has a fast-paced talk-rap. I like the Native Son verse better.
Chorus: The chorus has the exact same chords as Vertigo. However, this is where Vertigo dominates. The Vertigo chorus is more catchy and powerful while Native Son is more harmonic and raw.
Post 2nd Chorus: This starts out with, in my opinion, a short and cheesy string-bending guitar solo by the Edge. It is then followed by a similar rendition of the U2 delay-guitar found at the same spot in Vertigo.
Bridge: Native Son lacks the important post-bridge that exists in Vertigo ("all of this can be yours"). Instead, Native Son has Bono screaming "free" to the same chord progression as the post-chorus.
3rd Chorus: This is where it is confirmed beyond a shadow of a doubt that Vertigo is a better song. In the 3rd chorus of Vertigo, we find the climax of the song ("your love is teaching me how, to kneel"). This important climax is lacking in Native Son.
So Yes, Native Son is a great song. However, Vertigo is musically superior.