I would like to preface this by saying that the changes to champions and leveling are great fun, and I definitely prefer them over standard FE systems. Also adding necromancy stuff totally gets you into my pants.
Now on the the issue:
There are some staves in game that provide bonuses to spell casters, this was not an issue in FE, but in LH it's a problem if you've built your sovereign or champion solely for magic. The problem arises from the new tactical combat system for initial unit placement, which I actually really like if not for this gripe.
Since a staff is a melee weapon, it puts the character that I'm intending to use magic with (and in some cases is not equipped for front line combat) right into the front line. This is more of an issue later in the game when you're up against tougher monsters, but it is annoying early on as well.