I've been trying to think of how this could be fixed, and ultimately I think they just need to completely re-do how assignment of teams works, both on defense and on offense. I get that they're trying to encourage more involvement at the clan level, but the game simply is NOT designed for that to be practical, for so many reasons (*cough* chat system *cough*).
Instead what I would do is - for the defense side, have every player in the clan create two defense teams, and then have the clan leader/deputies assign those defense teams as they see fit. Similarly, for the resources, have all of the contributions of the players automatically be pooled, and have the leader/deputies assign them, instead of individual players. Realistically, this part of Siege is the least relevant for an individual anyway.
Over on the offense side, I think they should retain the interactiveness as far as combat is concerned - I don't think these should just automatically be resolved. But, I also think that choosing the fights individually is a bad idea, because participation is definitely not easy to either enforce or entice. What I would do instead is, similarly to the defense side, have each player in the clan come up with up to X offense teams - not sure the exact number, since I still haven't figured out how the mana tower rebattle system works. Then, the leader/deputies will pick from those teams and assign them to battle against specific enemy teams.
Once the team is assigned for battle, that player would get a notification ingame - maybe one of our favorite red icons or whatever - to indicate that they have a battle they need to fight. They'd have a certain amount of time to fight that battle - say, four hours from when it is assigned - after which the fight would just be fought automatically.