Here's my 2 cents on the whole EE system. I did almost all the EE trials, and a great deal of the EE wars until the past few weeks.
In general, the matchmaking sucks. I've had some good wars, and they are amazing, lots of fun, ups and downs, close calls, all comes down to xstal use and target choices, a GREAT way to war. The problem with that is I can probably count maybe 5 of these that have happened from the 50+ wars I've been in. This is greatly due to the 40 clans signing up of all different sizes, resulting in TERRIBLE option for matchmaking. With only a limited option of opponents you have no choice but to match people that are out of each others league unless you no match both. A war that has no chance, or a war that you sit on a pinned opponent is no fun to play at all.
So here's my suggestion for season 2:
Get more clans to sign up - you can do this many ways, offering a "Looking for Group" or mercenary system would help solo's that are wanting to war find clans, and also help clans fill in final spots for a war. Setting up wars in a pain in the ass, when you don't have enough signups, you want to bring in mercs, but not have terrible afk people. or rogue xstaller's. At the other end, when you have too many signups, you have to cut off regular warring people losing their chance for rancor/ee. Our clan has a large network that we work with, and it works great (thanks everyone who's helped) If KaW created a system like this it would help out the smaller clans figure out their rosters.
No force paid wars - Right now wars cost $2, unless you've reset many times, you're paying for xstals. This sucks. With less than 0.1% of your players participating in wars, you have a problem, and could probably make MORE money by offering "some" freebie xstals in game from a quest or eb. Get players hooked on warring and they'll buy xstals. Also possibly offer a "war xstal" instead that can be gained by EB's, or random player attacks. This won't bring in extra gold, ruining the balance, instead it'd offer players a way to try warring. People will war if they have 12 "war xstals" in their bank.
Matchmaking -Touchy subject... I said my thoughts above, but here's some suggestions for a fix.
BFA - This is HUGE in a war. War's are fought at 20%, and that is where BFA helps the most. Don't allow double/triple the BFA to war against eachother, obviously more clans will allow closer matches, but seriously, BFA needs a higher weighting.
BFE - This is starting to matter, and with more equip coming out the gap between old EB equip and fully enchanted war equip is big. This needs to be factored in, and hopefully without and easy exploit (naked signups).
Towers - This is another big one for wars - you HAVE to have spy D to war successfully. Some people wont try warring if they are hurting their plunder by building towers. Towers should be weighted fairly high so that clans with tower builds shouldn't be paired against a high "Eb Clan" that has no towers. I agree that towers should hurt plunder, you are building for war, not growth, you shouldn't get the best of both worlds.
KO's - Don't make random timed KO's (suggested in other thread), that's a terrible idea. It's only compensating for your server lag with incoming hits by trying to add a surprise attack. What could fix this much much better, is the same as other games, and have a "group spawn" where everyone who is ko'd comes up at set times, with a set % of troops (or for more interesting wars, full troops with a longer spawn time). Either that or allow players to have a few hits before they're open, to make up for your server lag.
General - I know your server lag sucks, but you have to fix incoming attacks. If you could actually do something about incoming attacks, it would make wars far more fun. But since that would require a big change, Would it be possible to show who is viewing your profile, same as other games, by knowing how many people are targeting you? either that or when viewing enemy profiles, show who they are targeting? Might give a bit of heads up, and having 15 people targeting you just before you come out of KO would give you a second to realize that it's a good time to have some team mates xstal. That way you won't need to show instant attack notifications, but they'd still be nice
TL;DR - Get more people to war, it will fix matchmaking.