Opt In / Opt Out / Leader Chooses
I'm seeing three possible solutions for this problem that desperately needs to be solved: Player opts in, player opts out or leader chooses who goes to war.
Lets look at the draw backs of each.
Drawbacks to Opting Out
A major drawback of players opting out (choosing to NOT enter the clan war) is that inactive players won't opt out and you don't want those players in the war. I believe that even low activity players won't always opt out and then not participate in the war. An opt out solution only deals well with active players that don't want to participate.
Drawbacks to both Opt In and Opt Out
A drawback with both opting in and opting out is the timing of it. If opting in/out is done for each war, it is best to allow a 24 hour window for clicking that button before the match making process begins. This makes the war duration go from 2 days to 3 days and no one will like an increase in time. The only way to deal with that problem is to cut the opt in/out time down to 12 hours and the war prep time to 12 hours, but those solutions have their own problems.
The alternative to opting in/out for each war is a toggle for opt in / opt out that maintains its setting until you switch it back. This isn't too bad, but I think it lacks the simplicity SuperCell strives to achieve in CoC. Players may forget to toggle their opt in/out setting and either miss a war that they wanted to be in or forget to opt out before going away. SuperCell wants this game to be as simple as possible and I don't think this option hits the mark.
As a side note, I don't see a problem with too many people opting in (in other words an amount that doesn't exactly equal an increment of 5). The same rule that currently exists can easily be implemented in this case: drop the lowest according to trophy count to make it an even increment of 5.
Drawbacks to Leader Choosing War Participants
As a side note, co-leaders should also be able to have this power since the concept of a co-leader is to provide a backup to the leader in the event that he is gone.
A drawback to a leader choosing the participants is that only an small group of elite members are chosen to go to war and other willing members are left out. I don't really see that as a big issue since people will simply leave that clan and go find another clan that allows active members to participate in the war.
Another drawback is that leaders may use the ability to participate in a clan war as a disciplinary action (i.e. for not donating enough) or a privilege to be earned (i.e. for new members). Either way I don't really have a problem with this. Again, players that don't like the way a leader leads can find a different clan. I believe that many clans will try to attract members by insuring that they can participate in the next clan war. It will become a good selling point for joining the clan.
Obviously my vote goes for leaders choosing who goes to war. The setting could be in the menu that allows leaders to kick and promote. Just add a setting to make that member a "spectator". The setting is permanent until the leader changes it. In the list of members, an icon could show up instead of the crossed swords that represents "spectator". This allows everyone in the clan to quickly and easily see who will be participating and who will be spectating in the next war. Time would not be a problem with the war sequence. this option solves the problems mentioned above in the other two options. The overall war time would still be 48 hours as it is currently. Inactive players would be dealt with as much as possible. They could be set as spectators by the leader waiting for them to show back up and let him know they are ready to join the war. The potential problems with this option seem to be far less than the problems with the other two options and are easy to deal with.
-Drew