Lilith's body and head exploded into LCL, while the failures are just fine. What
Do you really not see how there's a link between decapitated Lilith and decapitated Failures reaching toward Lilith's head? If you read my post on page 1 it will possibly make more sense
At risk of stating the obvious: the Mark.06-Lilith fusion we see becomes possible precisely because Lilith got decapitated, which makes Mark.06 the only real suspect for Lilith's beheading available to us at this time
I doubt beheading Lilith was a prerequisite, we see many other attempts by angels to meld with Lilith throughout Evangelion and they never have to cut off her head first. The fact that Mark.06 emerges vaguely from the head area of Lilith doesn't necessarily mean that's where he jumped in. In NGE when Rei melds with the mass production evas, her head emerges from theirs. It seems a very Anno-esque piece of cinematography to have the invading Mark.06 emerge from the stump of Lilith's neck.
The Failures were clearly the goal of SEELE and the twelfth angel/Mark.06 and I doubt having them be headless was part of the plan. For the failures to be missing a head from what appears to be a link to the decapitated Mark.06-Lilith, that most likely means that the decapitation was a deliberate attempt to halt the process of the Failures' creation/mobilization.
And in general, assuming that Mark.06 decapitated Lilith because it was the only hostile party we're aware of in our limited knowledge of that fight is a sort of simplistic view. There were likely many, many people involved in that fight, and I'm sure the drama was distributed across them.
I think the likeliest culprits for the decapitation, in descending order, are:
- a now retired Ayanami clone that defied its orders
- Touji (where else would he have died?)
- Kaworu (but why ? in 3.0 he apparently wants
people 'remade in the image of the fruit of life', which is what was happening with the Failures - why would he try to stop it back in the original attempt? and why did SEELE automate mark.06 instead of simply have him pilot it? would seem to imply they didn't trust him)
Also, the question of why Mark.06 seems to be stabbing itself is unclear. Would seem to imply warring souls within the Mark.06-Lilith body. Maybe Lilith somehow found her way in there after the events of 2.0. Also, two spears, one in Mark.06 and one in Lilith. Some of what happened is still confusing.