Well it hasn't implications for the gameplay.
I would respectfully disagree with that: one of the reasons top-down is common in the genre is because it makes it very easy to see exactly where towers are placed and how they align with other towers, paths (if present) and creeps. With a top down view it is also impossible for a smaller item to be difficult to see behind a larger one.
Isometric (whether traditional 2d or real 3d) can potentially suffer from both of these problems -- when the screen is busy it can be harder to tell at a glance if one placement is nicely aligned with another object, and larger objects can potentially obscure the player's view of smaller ones. This can result in player mistakes that may cause them to think the game in unfair.
My personal preference would therefore be top-down, for clarity.
If you do choose an isometric view I would probably recommend 3d with a fixed viewing angle rather than traditional 2d isometric -- the 3d is simpler and nicely avoids some problems that would have to be worked around in 2d.
Hope that helps!