Hmm... Personally for me, one thing I would like to see when it comes to full-time Spellcasters (like the Wizard and Sorcerer) is that they also have a number of non-magical options. So if we were say to take the 4e Power System for instance, they could have some Powers that don't have a magical connection, they certainly aren't amazing like Martial Powers but they serve their purpose.
Just to get away from the either Wizard does everything with his Spells, or the Wizard can only use a tiny little dagger or crossbow and does basically nothing with them.
I would like to see "Counters", so again using the Power system, your enemy uses a ability, it has say a Fire-keyword. You can counter said Power by using the Immediate-Effect that is recorded at the bottom of your Spells, the Counter in this case would be say a Spell with Cold-keyword.
I would keep what 4e is doing and divide up the Magic into various classes, so we don't have the Wizard that does everything. I quite like that we are as far as we know gonna get all the Wizard stuff into various classes, like; the Wizard, Illusion-clas (personally hoping it is based around Beguiler, my only spellcaster-class I personally used), Necromancer, etc.
This is more a pet-peeve and something I wouldn't actually see in D&D since it goes against lots of D&Dism. But the overabundance of elemental magic I would like to see decreased.
I think specific Spells, keywords, picking your Spells, etc. are very D&D things. So while having a freeform magic system be quite cool, it wouldn't fit the D&D feel.