Beezo, I'm so happy you reviewed these two! I just love the Alien franchise =)
I couldn't agree more with your assessment of the original Alien 3, and what it needed in order to stand on par with its predecessors. Shoving the religious aspect into the background was definitely a big mistake - a missed opportunity to give Ripley's journey and the other characters more depth (especially Dillon! Charles S. Dutton made a memorable character out of nothing, but it would have been even better to divulge something of his backstory, explaining what brought him to his faith. That would have given us at least 3 strong characters to invest in.) The only thing I would add is that Clemens really should have been the last man standing. He didn't seem to be much of a believer, so having him develop this crush on Ripley, and then seeing her and Dillon kill the beast, and then sacrifice herself - all that stuff would have stayed with him, and I think it might have been interesting for the next film in the franchise to follow Clemens.
The only place I really disagree is concerning the lack of coherence in the layout of the facility. You argue that Fincher dropped the ball, and normally I would agree that it's the director's job to create a coherent space, but I remember Jon Spaights talking about the "board game" he used to craft the first Prometheus script. It helped him work out the plot since he was able to visualize the spaces where the action was taking place, and I think it must have been incredibly difficult for Fincher to try to create that on-screen without having a finished script, so ultimately I blame it on that (I get the sense that you're unaware of script fiasco? At least, I don't remember any mention of it - maybe I missed it?). Even so, I think you make a solid point about the unconvincing creature effects and how it looked the same in each attack scene. I think Fincher could have done a better job of showing the creature, regardless of the messy script.
As for Q2's edit, I haven't seen it, but it was good to get your opinion on it. I agree that there is not a whole lot you can improve on as a third-installation of the series, but maybe it could work better as a direct sequel to Alien? I think at least one person has attempted that, and that's where I plan to go with it as well. It requires tweaking Alien first, to suggest Ripley has a daughter, and using scenes of Newt from Aliens in Alien 3, as if Ripley was having nightmares about Amy. The point is to setup her death scene so that it's intercut with Newt/Amy asking if monsters are real, and Ripley saying no, sweetie, and then falling down into the pit. I just think it would make her death very gut-wrenching if she did it to keep her daughter safe from real monsters (similar to the Gwenyth Paltrow/Morgan Freeman moment in Seven you talked about).
Anyway, I love the podcasts! Keep 'em coming =)