The ugliest are Gengar, Mewtwo X, Pinsir, Heracross, Aggron, Manetric (surprisingly), and Abomasnow.
I was extremely disappointed with gengar. I just can't believe GF thought that design was good enough to include in this game. I mean, it's the original ghost pokemon, why did you ruin it?!?!
Mewtwo X looks frog-like with webbed toes and gill like striations. It's another, huh???, design.
Pinsir's design is all over the place. The strange orange, blue, yellow, and brown color palette, discordant scarab-beetle wings, and oddly shaped arms and legs, just don't come together as a good design. Though, I do like the alteration of the spikes.
Hera cross has a shrimpish face with the long nose, awful orange/blue/yellow color palette, and gauche spherical arms. Plus, the best feature of the original design, the tusk is now uninteresting as it now is just one big spike. I don't mind the antennas though.
Aggron's mega should have been more sleek, instead they have added too much bulk which and uninteresting spikes that really don't convey a clear design concept. Reminds me of the awful gen 4 evolutions of gen 1 pokemon where they essentially bloat the pokemon add random tassels and such.
Manetric is perhaps the most unfortunate megalution. The original design resembles a hound with a "cool" and "formidable" faux hawk. In stead of perhaps elevating those traits by increasing his height bulk and adding facial hair to the mane, GF tastelessly placed a thunderbolt tumor on his back.
Abomasnow's design, like many others, is basically GF adding more spikes, tassels, flames, and beefcheesysupremeomegalicious crap. There is no thought or clever concept to justify their designs.
Though, I like a few mega evolutions, most of them, including others I haven't even listed in this post, are not good additions to the game. I like the idea of mega evolutions, however, like many, not all, gen 4 pokemon that added to previous evolutionary lines, there is a lack of taste. Bulking up a pokemon and adding spikes and random embellishments really takes away from a the clever and charming concepts that GF is known for.