I really have no issue with the number of ways to get waves done. 3 or 4 (normal battle, catapult, bombing, quest?) would be perfectly fine.
I do, however, think wars should happen less frequently. We currently have what, about 10 per year? Nearly 1 per month? Sometimes they happen for no reason whatsoever *cough, Turducken, cough*
Also, knowing the deadlines early would be pretty good.
And if we lose a war, we should face consequences. If it's a minor war, just no rewards would be fine. If it's a major one, deeply related to storyline, we should see some serious impact.
There's no need for multiple challenges or heavy investment is fancy art IMO. That'd just be a waste of time. A single challenge with good-looking rewards would be enough, or no challenge at all, really.
Music isn't that necessary either. Most forum players often listen to other stuff while warring, I think.
Wars that last too long bore me to death. Minor wars (say, a holidary war) should be made to last a week. Major wars, maybe two weeks?
Always having intro and outro custcenes would be nice. No need for flashy, time-consuming, top-tier animation, though. X% cutscenes would be nice to see, but they're not necessary either.
Finally, no Turduckens ever again. EVER.
This is just my opinion, though.