I think we can agree that certain aspects improved, certain aspects are a step down. This is evident in all TES games.
In Skyrim, the lack of variety in the schools of magic is evident. That's magics greatest flaw. Waterwalking, open lock, dispel, summons and a number of other spells were lost from Oblivion to Skyrim, and dozens of other spells have been lost since Arena.
Graphically, Skyrim is the best in the series. Fire looks like fire, lightning looks like lightning and all magic looks fearsome. Bound weapons have their own unique appearance, instead of having the same appearance as Daedric weaponry.
Mechanically, Skyrim has had some upgrades too. This area is a matter of opinion - whether you prefer the wind-up-and-hope-it-works style of Morrowind's magic, the press-to-cast of Oblivion's magic or the two-hands-shared-with-weapons of Skyrim's magic is subjective. I, for one, am a huge fan of dual-casting, especially with the Impact perk. We also have a greater variety of spell types (not effects) - constant stream spells, walls, runes and wards have been added in Skyrim, in addition to the traditonal on-touch, on-target and on-self spell types.
I'd say I prefer Oblivion's magic overall. There's simply a greater variety of spells, but lacks the 'hope-it-works' aspect of Morrowind's spellcasting. If Skyrim had Oblivion's variety, it'd take the cake for the best magic system in the series - IMO.