Generally either Modest (+SpA, -Atk ) or Timid (+Spe, -Atk). Naganadel has a high Special Attack and Speed (127 and 121 respectively) so it makes sense to boost these. Modest is great if you are going for all-out power as it boosts your Special Attack, and can be used in conjunction with a Choice Scarf (held item that boosts Speed) to be both fast and powerful. However, Timid is used more often as it increases Speed and lowers Naganadel's pitifully low Attack which will never be used anyway. A Timid nature can be used in conjunction with Dragonium Z to help Naganadel nuke something and hopefully kill it, enabling it to get a Beast Boost (ability) in Speed and help it out speed things such as Kartana (a hard counter). Here are two movesets:
Modest:
Naganadel @ Choice Scarf
Ability: Beast Boost
EVs: 252 SpA / 4 SpD / 252 Spe
Modest Nature
IVs: 0 Atk
- Dragon Pulse
- Sludge Bomb
- Dark Pulse
- Flamethrower
Timid:
Naganadel @ Dragonium Z
Ability: Beast Boost
EVs: 252 SpA / 4 SpD / 252 Spe
Modest Nature
IVs: 0 Atk
- Dragon Pulse
- Sludge Bomb
- Dark Pulse
- Flamethrower
Personally I would go for Timid as it will most likely make your faster than the opponent, however Modest is not to be ignored either!