There has been an inherant problem with the concept of this game from the beginning. The game is a spiritual successor to Master of Magic where magic is scarce and coveted like food stamps in a third-world environment. A small handful of people are in control of the magic pie, and have to sacrifice slices to let the magic spread. This makes it very difficult for the game to be heavy on the magic side, as it is somewhat gimped by its own backstory - and 'heavy on the magic side' is what most people seem to want (myself included).
Perhaps if we say that the rise of the channelers has opened up the floodgates of the worlds' magic? This way we can justify non-sovereign units having innate magical abilities, or learning spells or having magic-based attacks without a sovereign having to hand them a magic-stamp.
Shards should be treated like nodes in MoM. That way, if you get them, sweet, if not, no huge deal. Units should cost upkeep in resources such as food, gold, and mana per turn. So from the story side, we can say that the shards are releasing magic to the world, and tapping that power from the source has its benefits, though it is not necessary, and a person can still train as a wizard or spellsword without hoarding shards or being a channeler.
In this way, a channeler is to a wizard what a wolf is to a dog, so to speak (I'm sure there's a better example, but you get the picture).
This would take a lot of the restrictions away and untie a lot of hands when it comes to improving the game structure.
Having said all that, I still enjoy the game as it is, I just think that the above would make it way more fun.