One of the biggest problems, in my opinion, that they'll struggle to get over is the way the ride was marketed. Pushing something as super-terrifying worked great in the short term, it drew in the crowds. But now the marketing has died off, word of mouth has spread about what the ride is really like and people aren't that interested. Equally, as other people have said, trying to take the tone down the 'scary' path with over the top shouting, etc. has made it generally more hassle and unpleasant to re-ride than anything else.
I don't think the ride needs re-theming, the theme itself is great, ties in really nicely with the Nemesis story (even if the introduction video misunderstands a few of the points). Ignoring any technical issues with restraints that might need modifying, I think they need to take a good look at how the tone of the attraction fits together.
I'd ditch the 'abusive soldier' act but would still retain a human person giving a briefing. Treat the guests as they are supposed to be, civilians being invited to view the egg under heavily controlled conditions and re-write a briefing with that in mind. Reinforce the story to the guests in that briefing as well.
Gut the 'scare maze' ending, without actors it's pointless. Instead, re-dress it to look like an escape route/alternate entrance that has already been attacked by the creature. Damaged walls/windows, blood smears, stage smoke blowing out of damaged pipes (with compressed air blasts if you still want some occasional jump scares), red strobes, debris to make the path a bit of a zig-zag. Make it work as an ending without requiring any staffing.