Hi mate, see the following:
Armor
Avengers version has a cleaner armor (especially front thighs). The Battled Damage (BD) has way more accessories including battle damage pieces (chest plate, left arm, right bicep and shoulder plate).
Head Sculpt Accessory Included
Mark VI BD: Tony Stark sculpt in the helmet (with face plate options).
Mark VI Avengers: Full Tony Stark sculpt (exact same from the Mark IV).
The Avengers version is better if you simply want a very clean shiny piece to maybe pose in a Hall of Armor type display.
Value for your Buck?
For what you pay out there now, the Mark VI BD is better value for money and can be also be inter-changed with the Mark IV head sculpt, but is not part of the package. I am having difficulty putting it on at the moment.. hahaa.
The Avengers piece is nice, but lacks accessories. But I believe the Avengers piece does have less likelihood of suffering pink panties.