First of all, they're different Pokémon.
(Yay obvious statements)
But really, they're quite different and similar. They have different battling roles and while magikarp is everywhere, feebas can be a bit more tricky to find. However, they do have many similarities.
Even though both have the same BST, Speed, Defence, HP, base happiness, are evolved from fish, are "bad Pokémon" that evolve into "good Pokémon" and perhaps more, Gyarados is definitely a physical attacker, while Milotic is more on the specially attacking and defending side.
Feebas is also harder to obtain than the numberous magikarps in, well, just about every body of water. It's also harder to evolve, you either have to trade with an item or max out its beauty. With magikarp, just levelling it up to lv 20 is enough.
I doubt that they "changed magikarp's evolution style" to get feebas and milotic, since they have a lot of important differences. They are similar, but I'm pretty sure that they didn't mean for them to be almost exactly the same. Maybe they decided, "let's make another Pokémon like magikarp and gyarados!" but I'm pretty sure they wouldn't want them to be copies of each other.
Other differences:
-Milotic has an erratic growth rate, compared to Gyarados's slow growth rate
-Gyarados is Water/Flying, Milotic is just Water
-Milotic's egg takes 21 cycles, Gyarados only needs 6 cycles
-Speaking of eggs, Gyarados is in the Dragon and Water 2 egg groups, with Milotic in Dragon and Water 1
-Different movepool
-Different weaknesses, abilities, weights, heights, etc.
![Gyarados][1] ![Milotic][2]
Plus, they don't exactly look the same, do they?
[1]: http://img.pokemondb.net/sprites/black-white/anim/normal/gyarados-f.gif
[2]: http://img.pokemondb.net/sprites/black-white/anim/normal/milotic-f.gif
