Depends on the team
One is just straight up offense while the other can use set up and cause rage quits.
Mega Charizard Y
- Massive sp.atk at 159
- Access to reliable recovery (Roost)
- Solar beam covers 2/3 of its weaknesses and those are 2 fairly common types (Rock and Water)
- Overheat is beast in the sun with this thing
- Access to Tailwind provides for good support for teammates in singles and doubles
- Air Slash has that nifty 30% chance to flinch
- x4 weakness to Stealth Rock means needs a spinner almost all the
- 100 base speed isn't the greatest anymore
- Easily predictable moveset
- Although movepool is large, mostly physical so doesn't benefit Y much
Mega Charizard X
- Doesn't have that nasty x4 SR weakness anymore
- Eliminates electric weakness
- Access to Roost and Dragon Dance makes for a great set-up sweeper
- Dragon is a great type to have in the metagame
- Tough Claws means Flare Blitz gets boosted to a scary 351! Not bad at all!
- Unfortunately, no more flying type means no more ground immunity
- Susceptible to Lando-T (scarf) and Lando-I before a DD
- Intimidate almost completely stops the physical set
- The moveset DD, Roost, Flare Blitz/Fire Punch/Dragon Claw is completely walled by Heatran
Well, now you know pros and cons though I might have missed many.
In a nutshell: X is physical and Y is special and the non EQ X variant is walled by Heatran. Use what your team needs
Hope this helps!