The best method I can think of is :
1/ make your game with simple recangle, tweak it until you get the right speed, jump, fall... all the motion should feel right and properly balanced
2/ then, as you parallely developped a character design, you begin to flesh out simple key poses (4 key for a walk cycle, one for a jump, one for a fall pose). Just simple sketchs to test :
- the size of your character
- the rythm (you might change animation speed to fit the speed of your walking rectangle and avoid sliding walk)
- the poses themselves
- if you didn't destroy the balance achieve in step 1 (it could come from bad animation rythm or too unrealistic motion: imagine a human moving like super meat boy...)
3/ Once you get things right, you sketch the needed in-between (if you just have 4 keyposes and you put animation speed to 6, you might need to add some in-between to smooth the animation. animation speed to 12 should be better) - of course once you sketched the in-between, you test them because after all, a sketche is mentally easier to correct than a fully rendered frame
4/ You go wild and fully render your neat sketches OR you go 3D from there and try to fit your sketch the best as you can.
Yeah sketching is often better than going 3D too fast. 3D is great, but there's some thing you can find quicker with a sketch than disentangle your keys and curves. Some will probably say that they suck at drawing and moving bones is easier... You know... matter of taste :D
Oh and I tend to keep the rectangle from step 1 as a collision box, and just play anim on top of it with a every tick : sprite set position to spriteCollision (just example of naming)