Naanee and Floyd are obviously completely different WRs. Naanee has a career ypr of 8.9, while Floyd's is 16.9. You compared Naanee to Boldin, whose career ypr is 12.8. To me, Naanee reminds me of a guy best suited for a slot WR and possibly an H-back kind of role.
If Naanee was the #2 and played a lot of snaps split wide in 2 WR sets, his ypr would presumably go up, as would his TD opportunities. But Floyd seems better suited to being an outside WR, and Naanee better suited to the slot. And that seems to be how the Chargers are using them this year.
By game:
Game 1 - Naanee had 27 snaps - 16 in the slot and 11 wide; Floyd had 6 snaps - 3 in the slot and 3 wide
Game 2 - Naanee had 29 snaps - 22 in the slot, 6 wide, and 1 at H-back; Floyd had 8 snaps - all wide
Game 3 - Naanee had 23 snaps - 12 in the slot and 11 wide; Floyd had 23 snaps - 2 in the slot and 21 wide
Game 4 - Naanee had 23 snaps - 17 in the slot and 6 wide; Floyd had 26 snaps - 3 in the slot and 23 wide
Game 5 - Player Participation Log not yet available at profootballfocus
Not including game 5, Naanee has had roughly 2/3 of his snaps in the slot. Meanwhile, Floyd has had more than 80% of his snaps wide. I think when the log is available for game 5, it will confirm this trend. I also think it will confirm the trend of Floyd's snaps increasing. As someone said, he was very visible early in the game.
That data above would be even more interesting if we could tell where the players were lined up on plays when they were targeted. I suspect Naanee was targeted much more when he was in the slot than when he was outside, and vice versa for Floyd.
If the Chargers view Naanee as the likely successor to Chambers as the #2, I'm not sure why they aren't using him outside more, since that will be an important part of his job... it would seem that he needs to gain more experience out there.
I have been higher than most everyone around here on Floyd, and I think he has great potential. His problems are age and durability. However, if he holds up and plays well this season, I think the Chargers could probably sign him to a reasonably priced contract to keep him, and keep Naanee in the slot. Then they would be set at WR and could focus their efforts elsewhere, since they need help everywhere except QB and TE. I think there is a good chance this will happen.
If so, unfortunately from a fantasy perspective, the presence of Jackson, Gates, and good receiving RBs will probably continue to limit Floyd and Naanee next year and beyond.
For disclosure, I picked up Floyd in my dynasty league last week and plan to hold him while it plays out. Naanee was available earlier this season (not last week), but I passed.