Character wise: Naruto has the better storyline and character development. The story and characters themselves are remarkable compared to the often one-dimensional characters of DBZ. Goku's personality and intellect never really changed throughout the series from DB to DBGT. He was always characterized as that incredibly stupid but powerful guy who died thousands of times yet always beat the enemy (this is a generalization but you get the point if you watched DBZ). Granted, Naruto might be the same but at least Naruto started out extremely weak and then blossomed into the possibly the most powerful character on the show. He intellect has grown as well, shown in the battle against Pein.
Story-wise: Naruto wins. The story of DBZ got repetitive after the first saga:
1. Bad guy comes.
2.Goku fights him.
3 Goku starts to get beat and gets random power-up,
4 bad guy starts getting beat. Bad guy goes into powered-up stage,
5. Repeat steps 3-4 several times.
6. Krillin gets hurt/killed/ or some other character dies
7. Goku (or in one case, Gohan) unlocks a new Super Saiyan level
8. Bad guy gets beat peace
9. Repeat steps 1 -8
At least on Naruto, there is much variety of what happens battle wise and it always gets interesting and hard to predict what's going to happen (or least most times).
Battle wise: Naruto fights look better but DBZ fights are more powerful. You have people who can survive in outer space with no oxygen, whereas the most powerful person on Naruto created the moon. :| No disrespect to the So6P but Frieza destroyed an entire planet with a single beam. I'm thinking that wouldn't stand up much to the most OPed person on DBZ, SS4 Gogeta. And that's another thing, CHARACTERS CAN FUSE TOGETHER. That'd be the only real way a strong guy from DBZ can be beat is if two guys from Naruto fuse together and then, you'd have to pick the right two (i.e. like Naruto and Sasuke and not Konohamaru and one of his friends). Goku, died multiple times and still can back to win fights, even while he was dead. If Naruto dies, that's it. No more of him, on to the next hope. If somehow a character from Naruto was to beat someone from DBZ, they'd just be bought back with the Dragon Balls and fight the person again, and most likely win at that point. Just face it, those Saiyans are the most OPed characters to ever be shown in an anime/manga. As much as I like Naruto, they just don't stand a legit chance against these guys.