I think the only serious open issue on spells is figuring out what to do with crowd control spells.
In my original design, I classified the bulk of offensive spells as direct damage (DD), crowd control (CC) and save-or-dies (SoD). This, of course, might leave out some de-buffs and other miscelaneous spells, but generally speaking, I wanted to bring these three types to about the same level.
So, to fix DD, I added an amount to each damage die based on the level and added an extra effect based on the damage type. These effects still need a bit of work, admitadly.
To fix SoDs, I wanted to make them all take a full round to cast (not a full round action), to give the opponents time to react. This makes it more of a tactical desision ("Can I pull it off?") as opposed to a caster-always-wins scenario ("Roll a d20 or die, fucker!").
This leaves me with CC. Given the above two changes, CC seems like the obvious choice for your spell slots. A while back I thought of allowing a save every round to negate, but this results in more rolls and would require a lot of specific spell rewrites. I could do the whole full-round-to-cast approach of SoDs, but I'm not sure if it's too much. I think this would be my fall back approach in the absense of any other solution. Does anyone have any ideas?
Of course, figuring out which spells exactly qualify as CC is another issue, but at this point, I'm looking at the big picture. Also, I plan to tweak the DD damage-type effects a bit.