Hi there. I'm here to rate your team.
So by the looks of it this is an extremely powerful Hyper Offense team with Gothitelle, which I think fits greatly into your team as you can obviously eliminate certain annoying Pokemon (mainly Mega Venusaur). Aegislash and Thundurus-I work really nicely to keep hazards on your side of the field, Landorus-T provides you with a solid revenge killer, and Mawile is incredibly powerful.
However, looking over the team, and looking at your own notes, there's certainly some weaknesses to the team. Greninja as you've already pointed out is a pain, as is it for most offensive teams, due to it's coverage, speed, and power. I also think that Bisharp is another huge threat to you, as at 2 it destroys this team, and Landorus-T can't even revenge kill due to Intimidate giving Bisharp an attack boost. You also mention how bird spam causes you problems, but I think if you preserve Thundurus-I and Landorus-T, you should be fine (it's sounds easier than it is, I know).
Anyway, here's my suggestions.
1) Change your Deoxys-D to this spread. This set is purposely designed to beat Bisharp, but I recommend slightly changing it with Magic Coat > Mirror Coat, since you deal with Aegislash nicely with Landorus-T and Mawile (feel free to use it if you think you're struggling against Aegislash too). This can also really help you when Greninja leads off against Deoxys-D and goes for Dark Pulse.
2) Change Landorus-T to Garchomp. Scarf Garhomp I think would suit your team better, as it has enough speed to revenge kill Charizard-X at 1, can can switch into Charizard-Y's Fire Blast if need be. It's also still a solid check to Aegislash, and you're only really losing out on U-turn Intimidate. This will also slightly help you against Bisharp if it sets up to 2.
3) Change your Mawile set. Now there's two suggestions I have here, so I'm going to seperate each suggestion.
I honestly don't know how effective this kind of Mawile set is, but here's a few ideas you could change it to. Changing it to a Swords Dance set allows you to easily clean up late game, which your team kinda lacks despite being such an offensive team (I guess Landorus-T / Garchomp can cleam up late game, but locking yourself into Ground / Dragon STABs isn't advisable, when there are so many resists / immunities in the OU tier).
Another idea could be to replace Mawile with Assualt Vest Azumarill. Now here me out here, Assualt Vest Azumarill acts very much like Mawlie, as it still punches holes, but it offers your team a solid switch into Keldeo, Greninja, and Charizard-Y's Fire Blast.
Both options for the last change I think should be tested to see what best suits you as a player. Anyway, that's my rate. I hope I helped you out in some way, and good luck with the team n_n