A few days ago I was reading this interview on VLD S6 and one segment stood out to me:
Dos Santos: The initial idea behind this incarnation of Lotor was that you wanted to be able to look back on everything he said and see that there was a hint of truth to everything; every manipulation that he had, there was a hint of truth there. Maybe he snaps at the end, but when heās pleading with Allura, if she had said, āAlright, letās do this,ā I believe he would have been like, āOkay, great! This is working out. Planās coming together.ā
Montgomery: Lotor is a product of his upbringing and he grew up in the Galra Empire, so his method for going about things may not be as beautiful and peaceful as the Alteans, but his intentions were true. The funny thing is, had Allura reacted differently, it could have been an extremely different ending. But emotions were high and what Lotor did was unacceptable to her, soā¦
(This interview took place before the release of S7.)
I believe we were supposed to get exactly that extremely different ending, not in S6, but in S8, as a final reveal.
As I postulated in this meta, Lotor was possibly making use of the Entity by getting the Alteans on the second colony to accept it inside themselves, gain its powers and be capable of protecting their planet, purify raw quintessence and more.
In the final season, under the guidance of either Lotor or the Entity itself, Allura basically reaches the same conclusion, that in order to defeat Honerva, she needs to take the entity inside herself, to become one with the entity. Ta-daa! And thatās why LM says āthe funny thing isā¦ā because she knew exactly what that funny thing was and, later on, they would actually circle back to that same thing. And it would make sense from what JDS explains as well: āplanās coming togetherā. That was the plan. To beat Honerva with her own weapon.
Just as an exercise, try this experiment: put on the glasses of what I just postulated - that Lotor was actively infusing the Alteans on the moon colony with the entity. And then re-read the EPsā statements. I think they make much more sense if you start from that premise.