It's sort of unfortunate that I'm not at home to answer all of this (phone), but I'll give my opinion:
1. "Unnatural"
The series has dealt with various origins, natural/supernatural/artificial, for Pokemon since Gen 1. Grimer being essentially human sewage. Porygon being created as a computer program. Mewtwo being a clone. Magnemite. Voltorb. Ditto. Baltoy. Castform. Etc etc.
You know what defines a Pokemon? Being a Pokemon. No way around this, really. You can hate a design, you can say "This shouldn't be something", but it is. There's no superspecial "animals only/nature/no icecream" criteria for candidacy in the Pokemon pantheon beyond "It was concieved by Game Freak's mon team and placed in a mainline game".
2. "Formes in general are battle oriented only and are bad"
Not all formes spring from battle origins. Burmy's different formes are it using materials from it's environment to build it's coat. Basculin, Shellos are different colors based on their location, which expannds on Arbok's different hood designs. Castform was made to change with the weather. Cherrim blooms in sunshine. Giratina needs a way of moving about in the physical realm, hence why he needs legs in our world. Rotom is an electric ghost that possesses appliances.
Speaking of more specific ones (Deoxys, and other formes I don't know about), ya know... just because it's oriented towards battle doesn't mean it's anti Pokemon. You know what all Pokemon do? They battle, whether it's in a trainer vs trainer scenario or if it's between each other in the wild. It's no big surprise to learn that most Pokemon have features meant to scare off opponents, or attract mates, or ward off predators, or fend off opponents. That is, fighting advantages are part of the whole "animal" package.
3. "Unoriginal - megas taken from x"
You know, most every game has some feature that can be said to come from another game, besides the very first ones. Tamagotchi did raising pets first, most RPGs had the concept of physical/special attack properties, following Pokemon was done in Dragon Warrior Monsters (3 at the same time, even), Pokemon-amie is Nintendogs, and dozens of other ideas here and there have probably been done already in terms of world design, battle mechanics, Pokemon concepts, story details, and so on. Before you pick on this specifically, take a look back. Cross pollination takes place constantly. What really matters is that it's _new to Pokemon_.
4. "Unexplainable in-universe"
From the first game, there have been light themes of genetic manipulation. Beyond the concept of artificial Pokemon, Mewtwo was created spefically to be perfect, in terms of what? Combat, intelligence, strength. Fast forwarding to BW2, you have the scientist Colress, who was seeking to find a way to bring out the "full potential of Pokemon" somehow. By the end, he has apparently hit on a method involving the bond between humans and trainers. Now this may be unrelated, but the constantly-accessible Pokemon-amie and Super Training give indication that they follow from this research, as well as Mega Stones. Details will come forth, but nothing in the games is ever introduced just-so with no backing behind it.
5. "Digimon"
Mega Evolution has nothing to do with digivolution, or the Mega level. Even if it did, see the "unoriginal" comment. And third, Digimon complaints are just... you know, I have my own preferences for some mon series over the others, but it's seriously some 90s PvD stuff going on. My natural inclination is to not really take seriously any "argument" that uses Digimon as its core.
6. "This is not evolution"
It's stated to be something different than normal evolution (metamorphosis) - probably going to end up like some sort of overdrive. Having one active at a time is probably for double/triple battle balance. And the name choice is probably something someone in-universe came up with to tie it with something already understood, regular evolution. I also think that the difference is slightly more noted in the Japanese name, which is all katakana to draw emphasis and to strongly differentiate it from evolution, which is always in kanji/hirogana.
