This is just a list of suggestions I either came up with or read somewhere else and altered. Some may look familiar, others not, and a lot of these are big. So, here goes:
The War
We need a reason to be fighting the war in the first place, to satisfy part of the RPG component. my idea is that these two separate kingdoms have found the halves of an ancient relic, and are thus fighting over who should have the whole.
The magi enter here due to the kingdoms promising them a share of whatever the completed relic holds, thus meaning that the winning side will grow in power(gain a level) for winning, by taking the enemy kingdom's relic half from their paladin.
I also think there should be a larger variety in the types of troops in the waves. Currently all we have is your generic melee, ranged, and caster units. A little flavor with say, captain units, cavalry units, and both healing/damaging casters would increase the complexity and challenge in the war.
The Quests
Once the War has been won and the magi return to the home island, they will have the option to further unlock the relic's powers through a series of trials. Each element will represent a separate trial, with the main island being one on it's own and a tenth trial to represent the final challenge.
To progress through the trials, the magi must complete the previous one. In no way do I think this should affect purchasing elemental tiered gear, but just to add flavor to the RPG component. This would probably take the most time of any piece in the game, to develop and properly trigger/code a fun and interesting story with boss encounters, along with terrain changes to compensate.
The most obvious reward for these Trials is the gaining of levels and gold. Other rewards may include special gear rewards, such as improved elemental tier gear, multi-elemental gear, and neutral gear.
The Terrain
My main complaints for the terrain are that what we have feels cramped and there is a lot of wasted, unused space on the map. Solutions for this are difficult, as you have to also balance around terrain and placement.
I think that the islands need to be shuffled. Not just the quest hubs, but also the one the war is on. You could probably remove the portal island entirely by placing the way gates in separate areas on the main island, and also shove all the elemental islands together into a single island, divided up with the terrain boundary to keep them isolated from each other.
The shrines and farms could occupy their own corner on the map, out on their own where random creeps can't interfere with them, although this does remove players' ability to browse shops and buy/sell skill points during the war.
Other Thoughts
-Moving around as a mage with the current movement speed is tedious, and if the terrain gets an overhaul and made larger it would be even worse.
-Levels 15-40 suck in a game where the opposing team has one or more level 62. Perhaps a noob shield of say, 25-33% reduction between 15 and 30 would help.
-Town Portal Scrolls, for quickly returning to your side's base.
-I still would like to see a shuffle command added, or a system that will re-balance teams in a war automatically when they become uneven.
-More to come later, maybe.