Wizard Tower is just a really really strong card, in an already potent school, that plays to the major strengths of the wizard's wheelhouse.
All that to say:
The complexity of this "issue" is two fold. The wizard and the arcane school.
I'm a bit late to the discussion, but I think I agree with the above statements most. The wizard by himself is good, but not overpowered. The arcane school by itself is good but not overpowered. And the Wizard's Tower by itself is good, but not overpowered. By combining them, however, you get a really nasty and hard to beat opponent.
I think the wizard's abilities themselves are fine. They are powerful, but they cost mana to make up for it. The wizard's main problem is that his deck-building flexibility is almost unlimited. The easiest way to fix that would be to make the wizard pay triple for the element which opposes his chosen element (water = fire, air = earth), and for all War school cards. Without the element restriction, the long-rumored elementalist mage would be unnecessary, since the wizard could simply do the job himself (with the added benefit of still having access to Arcane spells). And the War restriction makes thematic sense.
As for the Arcane school itself, the 3 main problems are Teleport, Dispel, and Nullify. From what I understand, each of these cards is considered top tier in the meta, and have been for a long time. This hasn't really happened with cards from other schools, at least to this extent. In order to fix this, Arcane Wonders needs to design and release cards (from schools OTHER than Arcane) that directly counter these cards in order to reduce their popularity to manageable levels. It should be perfectly viable to build a competitive deck with absolutely no copies of those spells at all. Astral Anchor and Harshforge Plate are a good start, but it's not enough.
Last is the Wizard's Tower. I think the only things that should be changed are that it should cost a quick action to change out the tower's spells, and the tower itself should be epic. Being able to bring out another tower as soon as the first one is destroyed is just silly, and the quick action to change spells would bring it more in line with other familiars.