I thought before launch, Bungie said that there would be a regular strike and a Taken Variant, but i've seen multiple taken variants.

They Undying Mind

• Regular
  
• Endless waves of taken in the mid strike Choke point, but still have the large round vex thingy(can't remember the name), the objective was still the same (take out the vex thingy)
  
• Mid strike Choke point doesn't have the Vex thing, and the objective was to take out Taken Wizards

Valus T'aric

• Taken Everywhere, Killing Valus' Lieutenants replaced with killing yellow bar Taken
  
• Strike went back to normal at the Tank part
  
• Variant where there is no tank, and a ton of taken

These are the only strikes that I've gotten the "Taken" variants on, but I'm assuming there's others. It kinda looks like instead of having a true "Taken" variant all the way through, they came up with random variants of each checkpoint. So that in any given strike, you may get a checkpoint that is normal, then the next one could be 100% taken, or it could be normal with Taken invading it, etc.

EDIT: not complaining, I'm loving it. just trying to figure out what is going on, and see what others have come across

When I did the Valus strike, the tank was where things changed. You had to kill an invisible taken Gatelord.

Did a Heroic with Psion Flayers yesterday.

The first encounter which normally ends in one of the Major "Mini-Flayers" was replaced with Taken, as were most of the encounters up to the bosses. However, dealing with 3-4 Major Taken Vandals and a Major Taken Centurion is not my idea of fair and balanced challenge. Their random, reactionary, and staggered bubble shields to heal themselves and each other were ridiculous.

They also threw 3 Cyclopses in the second encounter, on the stairs. The second time I played through that mission the encounters were all Vex up to the bosses.

Definitely liking the periodic ammo crates in strikes, though. It makes it much more reliable to keep all your weapons fueled.