I can see Mega Zygarde being awkward to execute, mostly because of having to start in 50% form (or 10% if you got that dog in you). Base form absolutely needs Light Screen support in order to survive the many Ice Beams running around, especially Glaceon's. You then need full mega energy AND be in Complete form to mega evolve, so 50% Zygarde has to survive not only Ice Beam, but Dragon Rush, Ice Fang, Ice Punch, Moonblast, Outrage, etc. The stat swap Mega Zygarde gives will also be tricky to build around because 50% Zygarde starts with 100 Attack and 81 SpA, with no way to boost said SpA, so all of your special moves pre-mega will hit like wet tissue paper. No Coil in this game is also a damn shame, so this hurts non-Mega sets that would want to utilize the stronger Attack stat, or to live physical hits better.
The biggest issue is not being able to run Xerneas when using Zygarde, and I see the former still being the best restricted in S3.
My initial idea for a Mega Zygarde build is something like this:
Zygarde @ Zygardite
EVs: 252 HP / 4 SpA / 252 SpD (you could invest more into SpA if it turns out 50% can survive Ice Beams and Xerneas's boosted Moonblast just fine w/ Light Screen)
Modest / Calm Nature
- Core Enforcer -> Nihil Light
- Earth Power
- Sludge Wave / Focus Blast
- Protect
Max HP for a mon that eventually gains 216 base HP sounds odd, but you start in 50% form, which has base 108 HP. Not low by any means, but Garchomp's boosted Dragon Rush will still eat you alive if you don't invest in that 108 HP. While pre-mega, you hide behind Screens support to survive and become Complete, using Protect to block Ice-type moves. If Thousand Arrows actually grounded Flying-types in this game, I'd slot it in as a utility move to combo with Earth Power, but in ZA, it just hits them and that's it.
A physical non-Mega set would probably like Weakness Policy behind screens:
Zygarde @ Weakness Policy
EVs: 252 HP / 252 Atk / 4 SpD
Adamant Nature
- Thousand Arrows
- Outrage / Breaking Swipe
- Iron Head / Brick Break / Thousand Waves
- Protect
Zygarde needs dual STAB moves to deal with the Dragons and many Ground-weak Pokemon running around. Protect is also nice for Weakness Policy since the item can proc against a plus move while Protecting. The last move will depend on what you need. Iron Head, while it sucks, gives you coverage for Fairies and Ice-types. Brick Break for opposing screens while still hitting Ice-types. Thousand Waves could even be cool to trap foes in.
Unless someone else convinces me, I don't see a reason to use

form as the base.
Overall, Zygarde sounds cool on paper, but a lot is going against it, and I just don't see it replacing the non-restricted Garchomp, which has higher Attack, Swords Dance, and better item flexibility.