So a while back in my Pokemon Y game I discovered the mega evolution through the storyline and since then have been using it in every single battle that my Lucario fights in, and it only occurred to me recently that with great power usually comes a great cost. So I was wondering are there any bad things about mega evolving a pokemon?
Short answer: Yes
Long answer: It depends. Mega Evolutions arent 'better' (for the most part, I'll come back to this). They are just another way of building a Pokemon, similar to if you built a Pokemon holding a Choice Item, or Life Orb etc.
Take Gengar for example. Standard Gengar is still a powerful force to be reckoned with, and it's Ability Levitate makes it immune to Ground Type Attacks.
When Mega Evolving, Gengar changes it's Ability to Shadow Tag, making it impossible for the other Pokemon to switch out (bar switching moves like Volt Switch). But this also means that it regains it's weakness to Ground.
Now, if we simply compare stats, Mega Gengar has an extra 100 base stat total over it's Normal form, however most of this is invested in its already high Special Attack, meaning even neutral attacks that land on Mega Gengar are going to leave a large dent in its mediocre HP. Its stat distributions are:
Gengar (Total: 500)
Mega Gengar (Total: 600)
As such, the biggest con of Mega Evolving Gengar is the loss of Levitate. Ground is a very common attacking type, with Earthquake pretty much being a staple move on anything that can learn it. Coupled with the little to no investment in HP and Defense, Mega Gengar becomes an even frailer 'Glass Cannon' than it's Normal form.
But what about the Mega Evolutions that change their types?
Mega Charizard X is finally a real Fire/Dragon (Dragonite can stop laughing at him).
Charizard: (Total: 534)
Mega Charizard X (Total: 634)
It gets a large boost to Defense, It's (Physical) Attack is raised to be on par with its Special Attack, and It's Ability changes to Tough Claws, further boosting it's Physical Attack. As such, builds for Mega Charizard X tend to have powerful Fire and Dragon moves (as opposed to Flying), and with it's higher Attack stat Mega Charizard X can run either a pure Physical or Mixed attack set.
But unfortunately with the introduction of the Fairy type, Dragon isn't the overpowered type it used to be. Plus, Mega Charizard X loses it's Flying type, regaining Fire's weakness to Ground.
The con for Mega Evolving in this case, is again going up against the common Ground types, and the new powerful Fairy type moves which pop up more often than you think.
Side note: I've surprised many Dragons with Dazzling Gleam on Gengar ;)
So, in Summary:
Are Mega Evolutions 'better'? Sure, if you only look at the stat boosts, most if not all gain a buff to their stats, but this usually comes at a cost of opening up different weaknesses to exploit.
Does every team need a Mega Evolution? No. Most teams will work just fine without one. At the same time, most teams could incorporate a Mega Evolution and it would work just as well. Think of Mega Evolutions as just another way of building a Pokemon.
Note: Sometimes it pays to play the psychological game. If they think you're running a Mega Evolution, they may take particular steps to counter it, and you can catch them off guard. Sometimes it's even worth it to hold off Mega Evolving for a turn or two: for example, predicting an Earthquake with Gengar.
There are many Pros and Cons to mega evolution. First, the stats are changed. This can be good or bad. Lets say you are building a Physical Attack Lucario, but when he megas, he gains more Special Attack (Just an example, not 100% sure). Also, abilities change. Kangaskhan looses Scrappy for a Special ability that allows it to hit 2x per turn. But, then it can no longer hit ghost types. Same with Gengar loosing his Levitate. Also, types can change. Mega Gyrados switches from Flying and Water to Dark and Water. Lastly, the Mega Stone is a held item, so it prevents your Pokemon from holding a different useful item.
In my opinion, the benefits make up for the losses like 75% of the time, but that depends on the challenging Pokemon. Like my peers who answered before me said, stats change (never been a negetive thing for me), you lose abilities, which can suck sometimes, and types can change, which could be good or bad. I make sure I know what the changes are going to be for each Pokemon before Mega Evolution, that way I know before I do it if it is going to be helpful or if I'm better off without it (based on the opposing Pokemon's stats, type, ect.). I find that I'm usually better off not mega evolving Pokemon when they're under Lv.30ish. This is all just my opinion, I know people who don't mega evolve any of their Pokemon, and they're still great trainers, but personally, I'm a fan of mega evolution.