3d - Advanced Animation for 2d Isometric Game?

I need help with workflow suggestions for a flash game. (although the concepts would apply to other game engines, too).

In a game like: Hero Academy

There are several different character models each with a multiplicity of animations (walking, standing, getting hurt, attacking, etc.). I am certain that each of these could be manually animated and a sprite sheet generated and used, but when you add up how many animations and core drawings would be needed...that would be near insanity to complete.

So, in research I found that some are creating character models in Blender, Maya, a 3d engine of some kind - setting the camera angle to 45deg, etc. animating and exporting that sprite.

In each of these examples however, the character models were 3d looking i.e.: 3d to 2d

When I look at Hero Academy, they still look like a 2d drawing.

If I am looking to re-create a similar art style to Hero Academy and need several animations per model what is the most efficient/correct workflow to creating the animation? Manually creating each animation sprite in Flash? Or utilizing 3d and texturing it to look 2d?(if that is even possible)?

EDIT: Thank you to all those who have posted great answers. To add information to the concept, one 'issue' I am contending with is the modeling/view of our desired game. To further clarify, if you look at Hero Academy's grid system (a la chess board) if you wanted an entity to be able to move vertically or diagonally this would need it's own sprites. However, is this still a simple 2d side scrolling game since the camera is fixed? And they have simply designed the background map to have the EFFECT of perspective?

If that is the case, then using Nuoji's comments, a 2d skeleton would then again be possible.

The base question is: if we are looking at close to 100 different character entities all with their own movement animation, long and close range attack animations, taunts, etc. what is the most expeditious method of doing this?

Note that I have experience in programming but no design/modeling experience. Whether we went the flash animation route or 3d modeling route I would be learning from scratch so any previous skill or preference is nullified.

Answer

After looking at the trailer in your link, they are indeed hand-drawn sprites. The animation seems smooth, so I wouldn't be surprised if they used some sort of skeletal 2D animation. This style involves drawing the movable parts of the character separately, so limbs, head, etc are separate sprites and they are posed and rotated accordingly to create keyframes, and tween the animation by code.

The other method as you mentioned, would be to make 3D models and export their animations individually for use in a 2D medium. If you are familiar with 3D modeling, this approach can be a lot quicker. You'd make your keyframes and tween them as usual but you will be able to export the entire animation as a sequence of images ready to be used in your game.

Ultimately, it depends on the aesthetic you want to achieve. Skeletal animation isn't suited for complex deformations.