Should it have a Timid or Modest nature?
Or should it be a defensive Politoed with a Bold or Calm ability?
Because I want it to be part of a rain team and I need it in the lead
Well, it depends on your team comp. If you're running an offensive Rain team, I'd lean towards a Timid-Natured Politoad with Choice Scarf. Or, you can have a Modest Politoad with Choice Specs.
If you're running a defensive Rain team, then I recommend a Bold Natured Politoad, for tankiness against things like, Tyranitar.
Hope that helps. ^^