I actually prefer the civil war/human story lines to the metaphysical "Shivan-Vishnan" story lines, but those latter story lines were hardly introduced out of the blue in Tenebrae. Every single one of those concepts have their roots in either retail Freespace or Age of Aquarius/WiH1&2. Yes the Shivans/Vishnans are sort of the "gods" of the FS universe ... and that's why they're named after gods; that's why the original game Freespace 1 called the Shivans ... Shivans. They are the mysterious, inscrutable, avenging Destroyers. FS1 and FS2, FS1 more so, do have some metaphysical lines (especially the Ancients in FS1). BP, esp. AoA and WiH3 with a little in WiH1&2, continues and expands on that though it is still all technology and the humans/vasudans are sometimes able to copy it once they have a grip on what they've just seen happen.

Again I do prefer the more human story lines to the metaphysical ones and consequently enjoyed WiH1&2 the most. But if anything WiH brings more explanation to the previously purely inscrutable - it focuses more on the metaphysical, but with an eye towards making more apart of the universe than it was before.
I think the mission structures fit with the Fedayeen very well: they're a spec ops unit which has finally been unleashed by the UEF and are expect to be flexible in their abilities and operations. So you have one mission each incorporating a different aspect of the fifth column (though missing an infiltration/exfiltration of an asset

): a frame job, an assassination, an anti-terror-cell takedown, a combined arms battle, and a special forces assault. The story lines in each mission are all continuations of the ones from the previous WiH episodes and aren't meant to be viewed in a bottle. Just considering missions, Act 3 is fairly short and tells how the Fedayeen provide an impulse, a direction on each of the story threads. And the Dreamscape is the mechanic that then fills in the rest of the story including the final "mission".
I'll grant you that all the new mechanics could be overwhelming and it usually took me a few tries to get a hang of them each mission and the briefings were a lot more complex (sometimes difficult to follow). I'll also grant that I'm looking forward to a longer Act 4 with more missions and more of the standard Freespace space sim-style missions thrown in. But the new mechanics were interesting and I don't think because FS1&2 didn't do it that the BP team should be shy about introducing them. I liked having to think about them and how to use them effectively; acting as a commander or an assassin instead of a fighter pilot was a refreshing change of gameplay pace - a palatte-cleanser if you will that also sets up some mechanics which can be reused as appropriate during the course of Acts 4 & 5.
It is true that you get less invested in the other characters, but that is sort of the point. Al-Da'wa is a projection/amalgam of the Fedayeen and Laporte is an amalgam of her physical wingmen and is gradually losing her humanity (though actually her connection humanity is in some ways both what could've driven her mad, trying to destroy herself, but is actually also what saved her - i.e. Simms being alive). Even without the Fedayeen ... uniqueness, these are sharks, not soldiers. They are operatives. It's meant to be a different, more distant mentality. One thing was that the Falconer/Laporte friction is rather abrupt - the beginning part felt compressed - it arcs nicely as it thaws, but the beginning was a little off.
I also agree that Act 3 doesn't provide the emotional roller-coaster that Acts 1 & 2 provided and I loved Acts 1 & 2 as it told a more human story. But I thought Act 3 was interesting and innovative and felt very much apart of the overall story. While it tells a self-contained tale in some ways, in others it also is very much a "linker" chapter - i.e. that it flows best and feels less disjointed when viewed in the context of the surrounding chapters - another reason why I also can't wait to see Act 4 to see how the threads continue. Hopefully the current team will one day finish the final chapters and viewed as a finished product, I can easily see Act 3 fitting in to the grand scheme. Act 3 is almost like the FS2 SOC loops made a mandatory, integral part of the main story with more varied and inventive mechanics to go with being special forces. That's how I view Act 3 and I think it works brilliantly as that.
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My criticisms are touch more nit-picky: The GEFs in the first mission have to be sanitized for operational security, that should not really be a choice, and it was not communicated well that letting them live was letting them go entirely. I feel that was a mistake.
The aforementioned Falconer/Laporte friction felt off at first, some of the writing ... I dunno it seemed like references to stuff that got cut or just ... I'm not sure. The arc was fine.
Some of the new mechanics are bit buggy (like artillery stops responding to commands) and I would've liked a little bit more practice with them - i.e. a potentially neat idea would've been a short, optional training simulation before each mission to give you practice with the new mechanics when they could be explained in depth while you use them. I think this would also have helped then clean up the mission briefings a little as they wouldn't have had to explain them.
Those are my main gripes that come to mind.