The entire premise behind "picking your battles" is that battles are expensive, and hence, you can't afford to fight every battle. But in a highly functioning team, bringing up suggestions and points for discussion shouldn't be expensive. It should be natural and fluid, with every person in the team expected to voice suggestions and concerns whenever they see them. In a team where people aren't constantly trying to jockey for position, where people are open to discussions without getting caught up in their egos, having people bring up suggestions freely is of great benefit to the team and the project.
Maybe the real question that needs to be asked isn't how to "pick your battles", but rather, how to build an organization where people can contribute suggestions and concerns, without getting themselves dragged into a battle.