If you will make 1 sprite with 50 animations you will get less download size, because construct will place all the assets in the same sprite sheets.
If you will make 50 sprites with one animation each - you will get 50 sprite sheets - longer download time.
But making 50 sprites may be better in a manner of structure-simplicity, much easier to put each soldier in his family according to his abilities, so you will code according to families and not per separate animation cases. You may even earn in terms of performance because you will pick more specifically in your conditions.
If I was you I'd use 50 sprites with one animation each and place them in families (soldiers (all), land, air, fast, giant, regenerating, spawning etc...)
And later it will be much easier to add new soldiers, you will have to just add the unit in the right families and set some family variables, without touching any code.
p.s. More over, what if you will want to add more animations to a unit. Right now you have one animation - walking, but you may want to add animations "die" and "attack"... So yeah, use 50 sprites.