Well if I was going to join any of the bad guy organizations it would definitely be Cipher. They were arguably the most successful and connected organization in any of the games. They corrupted cities, politicians and Pokemon what more do you want?
I want them to not lose to kids that look younger than ten years old. :V
BTW IT WAS TEAM SNAGEM THAT FIRST CREATED SHADOW POKEMON NOT THE CIPHER ORGANIZATION.
...no, I'm pretty sure they just stole them, and Cipher did all of the Shadow-making.
As for the topic on hand... well, I think Megas do get a better boost (100 to base stats in total? Sometimes a bonus ability and typing change to benefit from as well?) than what Shadow Pokemon get (new moves that aren't necessarily better than what they would normally learn, mind, super effective on non-Shadow Pokemon). But in terms of concept, I prefer the Shadow one. Mega seems rather region-specific at the moment, but Shadow Pokemon introduces an interesting bunch of concepts. Pokemon battle with friendship, but go the other way and the result can be terrifying. Mega Pokemon require a stone or two, and the effects only last the battle. Shadow Pokemon?
They remain shadow, until you work hard enough to get on their good side. And even then, you need the help of Celebi/Relix Stone, or a whole bunch of science (Purification Chamber) to totally reverse the effects. And Lugia was not far off from being unpurifiable to boot. And Mega Pokemon have control over their power - Shadow Pokemon may just as easily turn on trainers.
In terms of concept, I feel Shadow Pokes are more interesting to me. And they're probably the ones I'd like to face
less than Mega Pokemon if I was an actual Pokemon trainer. Thankfully I'm not. =p