Overall there is a 273 Resilience and PvP Power difference between the Malevolent and Tyrannical gear. The reason the PvP stats on the Malevolent gear is so high is because of compensation for the lowered item levels on the Season 13 Honor gear comparitively to the Season 12 Malevolent gear.

I explained this in a previous post, so I will quote it here:

14/02/2013 12:38Posted by Nakatoir

• 5.1 Malevolent Gear has a higher ilevel than 5.2 Malevolent Gear.
• 5.2 Malevolent Gear has more PvP Power/Resilience than 5.1 Malevolent Gear.
• 5.1 Malevolent Gear
• 483 ilevel (491 with 2/2 upgrades)
• ~30 ilevels of PvP Power and Resilience
• 5.2 Malevolent Gear
• 476 ilevel
• ~36 ilevels of PvP Power and Resilience

That explains the high PvP stats on the season 13 Malevolent gear. When you consider that the Tyrannical armor for season 13 does not receive this compensation, its PvP stats are slightly lower, but the base stats on it are much higher and in the end it is an upgrade for your character. For a comprehensive comparison of these items, please check out WoWhead.
(This is a comparison of the Monk Ironskin sets using non-upgraded S12 gear, so feel free to change it to your own class)

Can someone please confirm if this is intended or not???

This is intended, at this current point we have no plans to change the stats on the current gear sets.

14/03/2013 10:39Posted by Thornass

Thanks Nakatoir, and now that I'm back from an unfortunate ban, I'd like to ask you what your opinion is on the stat difference between the s13 Tyrannical gear and the 5.3 PvE gear. While you miss out on PvP stats, the ilvl from the PvE gear is so much higher that it might outweight PvP gear for certain classes. What do you think about this?

Sadly I cannot give much of a comment on the difference in stats as the 5.3 gear is yet to be released. I can say however that we want to try and make sure that going into all future patches, including this one, that gear rewarded through PvP remains the best for PvP purposes. We understand that the community is concerned with PvE gear returning in PvP and we will do our best to prevent this.

As for the 5.2 gear difference, I am going to assume that you are concerned with Heroic gear. As you can see on these Hunter sets, while the main stats are lower, the survivability and damage increases caused by the PvP stats compensate for this, and then some. The equivalent budget given to these PvP stats would be approximately 40 Ilvl's, which is quite a lot.

I totally misstyped me there, thank an all-nighter for that. I meant 5.2 Heroic PvE gear. Especially openers from Rogue teams (mass stealth) might totally gib the enemy teams within the first few seconds. We will see how it goes, I guess. ;)

No biggie, I assumed you did and that is why I mentioned 5.2 in the post ;)

But just to quell some of your concerns in the area of damage, this is something that we are keeping an eye on and will make changes as they are necessary.

20/03/2013 09:00Posted by Thornass

This is not hating, it's the majority of the community asking for a fair environment and a fresh start of the season.

If you check our most recent hotfixes blog, you will find two key changes that we have made to help with these issues of gearing. I will list the two changes we made during the maintenance here to make it easier to find:

• PvP
  
• Season 13 Tyrannical weapons had their item levels increased to ilevel 498, up from ilevel 493.
• Season 13 Malevolent Honor gear now gives more Stamina.

These changes are designed to make S13 Malevolent armor equal to its S12 counterpart as well as making the Tyrannical weapons equal to the S12 2/2 elite weapons. This should help greatly in resolving any remaining gear disparity issues from last season. :)

The obvious order of things should be:

Elite Conquest > Conquest => Heroic > honor => normal > LFR

This is certainly not the case currently!

This is actually how it is intended to be and also how the gear currently functions. While the resilience and PvP power of the Conquest gear is slightly lower than the honor gear, the overall stats on gear are what results in it being an upgrade. Even if it is not apparent immediately just from a quick look, the Conquest gear is better than the Honor gear that is currently available.