Honestly, I think some of the things that need to be fixed have nothing to do with clans at all. They have to do with the mechanics.
Issue: Rosters
Possible Fix: Battle and Siege servers go offline five minutes before a strat battle for strat preparations. If one side fills their roster, and the others do not, the players are funnelled onto the other team's roster until it's full. Downside, yes, 'bad' players may be put on the unfilled roster, but in all honesty, the merc advantage of the other side would likely overpower the unfilled roster anyway. In close rostered battles, this becomes an issue... But when it's 30 vs 10, the other side needs the people.
Issue: Crime
Possible fix: Either reduce the rate in which troops are lost, or install a different kind of fix. For example, troops lost to crime increase the population. If the population goes over 'x' percentage in comparison to the garrison, there's an AI revolt. Either it's an actual battle, or the fief simply 'turns.' Silver drops to 0. Original strat equipment is in place, yada yada wolf wolf.
Issue: Alliances
You can complain all you want about alliances, but in all honesty, nothing will change. If you have 100 little factions, there's nothing stopping them from 'blocking' together.
Issue: Faction size (Anti Annexation Proposal Explained)
Possible Fix: Don't allow people from different factions to join other factions while maintaining their original banner. IE an Astralis member joins the Squids in Strat, but stays in Astralis (Yes, it happened). This would stop a lot, but in all honesty, if someone wants to be in one mega faction, they'll end up there somehow.
Possible Fix: Limited Ladder Sizes. Yes, make people make decisions on who is in their faction rather than allowing anyone and everyone. How many times have we heard Kesh say '8 man faction..' and heard other people (myself included) say that ladder size doesn't denote activity.
Issue: Economy
Issue: Themed armies
Honestly, there's no way to limit the gear someone uses. When the winning army leaves the field, they have looted gear. There's no way to stop them from using it. And in all honesty, they shouldn't have to. ;-) Since gear degrades, I'm all for keeping armies in play rather than having them fight twice, and have to go back into trade mode to re equip themselves.
Just some thoughts.