According to this datamine of the most recent APK, there are a couple mechanical changes to encounters.
Code has appeared fleshing out the CRITICAL CATCH mechanic which first appeared in the previous APK but has not been implemented. The following components now appear:
I can not confirm whether these have actually been implemented or not yet, but according to this Silph Road reddit thread, they have been:
Critical catches have been implemented. You know it's a critical catch when the ball immediately drops on the ground after hitting the Pokémon and has 4 rays of light leaving upwards in a zig zag motion.
Additionally, as @Rapitor has mentioned in the comments on the question and as I have personally witnessed already, Pokémon now move in more directions than up to mess up your throws. They can move side-to-side (which unfortunately makes their CP go off-screen if you have AR-mode turned off). From that same datamine, it seems there are other states that they can be in:
It appears the way Pokémon interact during wild encounters has been upgraded. There are now several movement types at play rather than just 'wait', 'jump,' and 'attack':
According to the same Reddit thread as above that confirmed critical captures, it appears that different Pokémon tend to move in different patterns (probably explains the naming conventions chosen):
Pokémon move in new ways during the catch sequence. Ledyba will move in a "V" motion, while Qwilfish will move sideways form left to right, with their catch circles following them. Other users in this same thread also report new movements for gen 1 Pokémon like Venonat or Abra.
Another change worth mentioning is that you are still only able to use a single berry at a time during a Pokémon encounter, as mentioned in the (same) Reddit thread:
You can only use 1 berry at a time on a Pokémon. So no, you can't use a razz + a nanab on a Pokémon. The active berry is used as an icon on the Pokémon. Once the icon disappear, on a failed catch attempt, you can use an another berry.