The eyes still don't quite look right.

 Here is my edit:

 

 Of course he is looking ahead and not down now, but IMO it looks more like Mario.

Secret of Mana sprite:



Your sprite:

#2

I am critiquing this one because I think its the better of the two.

Shoulders way too broad, she looks like a body builder.

Head is about 1/3 the body size on yours, on the SOM sprite its about 1/2 ( vertically ).

Waist is about 1/2 size of head, and legs are about 1/2 size of head ( vertically ).

The perspective on yours looks like its from the front only. This has to do with the head / body / leg size ratio.

Color on yours looks good, but the shading seems a little thick in some places like on her mid-section.

 The right arm on the jumping animation bugs me. The forearm is doing something weird when he falls back down.

 I am not sure if it should be horizontal like that.

 Other then that it is great.

 The dino is nice, but it looks like someone shot a missile through his nose.

Ya, I agree the top part of the sprite looks like its out of sync with the bottom part.

Also the top part is leaning forward while the legs are curled up under him. The legs should be farther back. Of course, I never played the game so don't know what the sprite your are emulating looks like ( post it maybe? ).

And yes, looking at your avatar you should know better 

SolidSnake is a great name.

Haven't made any stuff lately because of my eye and health problems .. simple old school animation, Black border sprite at 20x20 size <except for the attack>. 18 colors for the first version, then made it down to 12. Is it readable for it's size?

 This is nice.

 I think if his shield moved down 1 pixel in the second frame of the walking animation it might look better.