Yes Eva is super deep and i,ve done much research on the identity of the 17 angels, the role of lilith, dead sea scrolls etc. good stuff.

OK...this is my take...Spoilers galore!!!!!!!!!!!

The last 2 episodes are NOT alternative to end of eva...they are simultaneous and just as important. This is human instrementality going on in the chracters heads, and then mostly Shinjis. They happen on a spirtual and celestiaL level during end of eva...Shinji perhaps experiencing this in his head while he is going mad before the 3rd impact and during the 3rd impact when God speaks to him through Rei and Kaworu.

I do not know how exactly this goes on, but they reflect the perspective Shinji wishes to see in whiich he does the right thing and is congratulated. This is a very happy end, completly different to the reality that Shinji realises at the end of eva(which is why he cries and realises his mistake in restarting humanity).

Ok, the objectives

Seele, wants all life to end, that was there plan. They saw death as the answer to lifes problems, as salvation.

At the end of eva, it is my opinion that Shinji wanted this outcome, but was convinced by God not too. So he restarted humanity.

Commander Ikari wanted human instrementality...to fuse all creatures as one. This would have reunited him with his wife (whos spirit was dorment in Eva 01) and solved all problems in his opinion.

P.s- Behold the Void...i consider Eva the ultimate mind ****. So if Raxephon is even more so...why is it you do not like it?