"Ori and the Blind Forest," side-scroller that recently caught my attention:

http://www.polycount.com/forum/showthread.php?t=135747

(as my statement that "no, side-scrollers are not too common.")

Side scrollers are overdone precisely because side scrollers are easier to do (to modern production value and gameplay standards, that is).

+Skeletal animation is simple in a plane, top down games usually need traditional animation which you can not afford to do with any significant quality or variety (only studios with real funding can do this)
+Character is easily visible (contributes to player-character relatability and satisfaction with the game)
+Characters are easier to draw from direct angles (cheaper art- WAY cheaper art, and less suck because artists are more competent at this)
+Environment is easier to draw from direct angles (Again, cheaper art, and less suck)
+View is easier to manage as a flat plane into the world (lack of 3d elements means there's nothing hidden which it difficult to show- makes programming and designing gameplay easier)

There are so many reasons side scrollers are easier than top-down (or isometric) games. But that they are easier is why they are overdone. Not because people randomly chose to overdo them.

+Skeletal animation is simple in a plane, top down games usually need traditional animation which you can not afford to do with any significant quality or variety (only studios with real funding can do this)

What? No. You can use skeletal animation with top down just fine, and in fact it may even be more suitable there than in sidescrollers (since you don't need to cheat with the angle the player is looking at in top down). Just apply a different worldview transformation (and keep the orthographic perspective). There really isn't much more to it.

Determining what's visible by the camera is more tricky, unless you can afford to scan every object (although with the scenery you can cheat and make it a pure 2D grid graphics-wise).

What? No. You can use skeletal animation with top down just fine, and in fact it may even be more suitable there than in sidescrollers (since you don't need to cheat with the angle the player is looking at in top down). Just apply a different worldview transformation (and keep the orthographic perspective). There really isn't much more to it.

I don't know what you're talking about... are you referring to 3d assets?

This is with regards to 2d games, e.g. 2d skeletal animation.

For example, with a software package like Spine: http://esotericsoftware.com/
Or a custom solution.

With 3d it doesn't matter (but see the thread subject, this thread is about 2d games, not 3d games with orthographic projection, which is a very different thing).

"Top down" is, as in, older Legend of Zelda games, like Link to the Past, which feature a 45-ish degree angle to the ground, and the character with the ability to walk "up" into the scene, to either side, "down", and sometimes at 45 degree angles too (relative to screen space), although in LTTP diagonals used the cardinal assets.

Skeletal animation can not turn a character facing the player (walking down) into a character walking "up" or "left". Every direction must be drawn and animated independently.

This perspective also involves a much larger degree of foreshortening, which is difficult to achieve in standard skeletal animation and creates unsightly distortions when applied to more than 20% or so of the limb's length.

If you want, I can break it down more fully and provide more examples of what works and what doesn't.
I'm guessing you meant 3d, but if not, I'd love to see an example of 2d skeletal animation applied to the "top-down" perspective of free roaming adventure games.