Much of the film is Kaworu using his devil's tongue to lure Shinji into blindly going with Seele's plans. What's made clear is that the change in Spears made a big enough difference in Seele's scenario for Kaworu to abort, albeit too late for Seele. What's not clear is what difference the change in spears actually makes to Seele's plans. Just like when they used Kaworu to interfere with Third Impact at the end of 2.22, it's clear that they don't want just any old Impact; they're after a very specific version of an Impact.
To begin exploring this, we have to consider a few things. First and foremost is Gendo's farewell to Seele in Q.
01:16:29 {Gendo} This is farewell.
01:16:33 {Gendo} Though you have all changed the form of your souls,
01:16:37 {Gendo} you are still creatures blessed with the Fruit of Knowledge.
01:16:41 {Gendo} Though you could have lived for an eternity,
01:16:44 {Gendo} you can escape the fate of death no more than us.
01:16:50 {Gendo} To advance the evolution of the flock burdened by death,
01:16:54 {Gendo} you gave us the gift of civilization.
01:17:00 {Gendo} On behalf of humanity, I thank you.
01:17:04 {Gendo} Let death return your souls to where they belong.
01:17:12 {Gendo} The long desired Human Instrumentality Project,
01:17:15 {Gendo} and the inevitable deicide, will be completed by me.
01:17:19 {Gendo} Rest assured.
01:17:21 {Seele 01} Our wishes have come to fruition.
01:17:25 {Seele 01} Good.
01:17:26 {Seele 01} All is well now.
01:17:29 {Seele 01} We wish for Human Instrumentality, the peaceful purification of all souls.
This conversation implies that Seele is really old, and that they were responsible for civilization. It's also implied that they were once humans, based on them having changed the form of their souls to extend their lifetime, and this is supported by the fact that they choose to also join in Instrumentality.
This conversation also harks back to Kaworu's explanation of Third Impact earlier in the film.
00:50:58 {Kaworu} In fact, they help drive evolution.
00:51:02 {Kaworu} Life has always changed itself to adapt to the world around it.
00:51:08 {Kaworu} However, Lilin change not themselves, but the world.
00:51:15 {Kaworu} So they brought the rite of artificial evolution unto themselves.
00:51:21 {Kaworu} Old life is offered in sacrifice,
00:51:23 {Kaworu} so that new beings blessed with the Fruit of Life may be created.
00:51:29 {Kaworu} All this is an act of extinction that has been programmed since time immemorial.
00:51:33 {Kaworu} Nerv call it the Human Instrumentality Project.
"Lilin change not themselves, but the world". This could be a reference to the Fruit of Knowledge and the civilization that was bestowed upon humanity by Seele. The goal of the Human Instrumentality project is to create new life blessed with the Fruit of Life.
This raises some questions about Third Impact and the Failures of Infinity. While the events of the fourteen year gap are intentionally shrouded in mystery and will continue to be, I wonder about the nature of Near Third Impact (which we see in 2.22), versus actual Third Impact, which is what results in the Failures of Infinity. As established earlier, Seele interfered with N3I because it wasn't what they wanted; it was an uncontrolled Impact manipulated into happening by Gendo, and they stopped it using the Mark 06. Based on what we see in Q, it's clear that it was started up again, and that the Mark 06 was involved at the center, after somehow being made autonomous (perhaps by Dummy Plug, or possession by the 12th Angel). Asuka also has a line, however, saying Third Impact will start again if Shinji pulls the spears, implying it was stopped again before being completed. All in all, it appeared to be another mess that was aborted, but the end result was the planet being left the way it was, and the FoIs being created. Are these the beings blessed with the Fruit of Life Seele is looking to become? Or is this still not what they want? Why did Third Impact stop?
What we do know is that Seele didn't release their souls to be gathered for Instrumentality when the FoIs were created. We also know that Kaworu doesn't appear to have been directly involved in the Impact, due to the Mark 06 having been made autonomous. Was Third Impact set off before they were ready? I speculate that Gendo had a hand in sabotaging their plan with the Mark 06, and that it was probably Misato and co. that aborted the Impact. Either way, it does not appear to have gone the way Seele wanted, hence the next fourteen years of planning for them. Perhaps the FoIs were their original plan, but was screwed up. Perhaps their plan was hijacked by Gendo yet again, and the FoIs have nothing to do with Seele.
I feel I've gotten no closer to an answer regarding Seele's intentions in the Rebuild series. And now that they're dead and out of the way, we may never know. But maybe in 3.0+1.0 we'll get enough details to fill in the blanks a bit more.
*script found here: https://github.com/eva3/Evangelion--3.0 ... RANSLATION