Basically if you can do your animation in C3D (without using morph targets, which currently don't work in Unity) then it will faithfully work in Unity.
C3D's problems aren't so much in its capabilities (which essentially allow you to do anything) but in the interface around those capabilities (which is rudimentary).
E.g. you can't select keyframes across multiple objects (if you wanted to clear a bunch of them at once, or drag them to a different time) OR on one object across time (if you wanted to adjust timing for a series of keyframes). More capable 3D programs let you do both (at once).
To make a simple analogy -- both Photoshop and MS Paint let you create and edit 24-bit color images, but in Photoshop you can adjust the hue of an entire image by adding or changing an adjustment layer. In MS Paint you'd need to modify each pixel manually and use a pocket calculator or a lookup table. C3D is (unfortunately) a lot closer to MS Paint than Photoshop in terms of its animation workflow.
So, returning to the example: you've animated a really cool wrestling move, but -- after looking at it closely -- you decide that a particular arm motion occurs a little too soon in the move and that a secondary motion of the head just looks wrong and needs to be removed. In most high-end 3D packages you'd simply select all the keyframes relating to the arms at the appropriate point in time, drag them a little, and iterate until you were happy. Then select the range of keyframes (in time and hierarchy) that relate to the head move and press DELETE. If you decided you DID like the head move after all, you could perform a single UNDO.
In C3D you'd need to select and move each bone's keyframe manually for EACH adjustment of the timing, then you'd need to select each keyframe of the neck-to-head hierarchy for each keyframe and delete it manually. You'd better be sure, because who knows how many steps you'd need to UNDO if you changed your mind.
Now, realistically speaking, good animators spend MOST of their time making these kinds of adjustments to timing. So for this extremely important use case, C3D is -- well -- crippled.
Final Note: if you're animating entirely in IK using IK targets, C3D is (I assume) a lot less annoying since you only need to keyframe the IK targets (at least, until you're pretty happy with the results). Unfortunately, I know of literally ZERO animators who rely 100% on IK. A huge amount of animation work is FK, and this is where C3D's interface is most seriously broken.
OK, I lied, an even more final note: an even more common use case is "point to point" -- one of Disney's golden rules of character animation. The idea is when a character does something (e.g. reach for a vase) he/she should spend most of the time near the key poses (preparing to reach, reaching) and very little time in the transition (stretching out his/her arm). 3D animation programs tend to linearly or cubicly interpolate between poses. This is at best OK for a single A to B action, but absolutely terrible for a series of three or more. The usual way to fix this is to animate from A to B, then pick points A1 (close to A) and B0 (close to B) and drag them close to the middle (so A slowly goes to A1, then quickly to B0, then slowly to B) -- classic point-to-point. Since you can't drag keyframes belonging to multiple bones across the timeline, this very common, simple use case is -- again -- atrociously broken in C3D.
Related Threads
http://www.cheetah3d.de/forum/showthread.php?t=1512
http://www.cheetah3d.de/forum/showthread.php?t=1612
http://www.cheetah3d.de/forum/showthread.php?t=2044
