The only real issue I have to say from being around the ride yesterday was that the banging of the final area was very audible from the surrounding area, and I can't help but think that if you were to remember that when beginning the ride you'd be a bit confused as to why the monster has suddenly gone back into it's egg, and all is fine and dandy :P But I guess I'm looking into this too deeply, and no doubt the noise is rather obstructed by the baggage hold when in the main queueline.
The general reaction of guests leaving the attraction looked much more positive than those of opening day, and there were certainly people who looked more than glad to be free from the last container.
Going from feedback others have posted I can only really think of a couple of things which may benefit riders.
Firstly, in the final lift a few people have suggested that it seems rather odd you empty out into this "decontamination area" even though you are meant to be in a facility which has been reasonably adapted for the public. Maybe the addition of either a recording, or even just a couple of spoken words from the two staff who are on the other side of the doors explaining that you have been taken out of the lift at an emergency exit of some description due to the monster preventing the lifts going any further, and that you will now be passing through a decontamination area to ensure you are safe to leave the facility. Or something similar to that effect, just to plug the hole in the story for anyone wondering.
Another idea, maybe that once the groups are making their way to the new area some screams are heard from behind them, either recorded, or by the staff followed by some sound effects. This would give the illusion that the monster has gotten to them and attacked, which would also add to the panic and fear of those leaving.
Lastly, how about adding some kind of lightweight push door over the end of the container? The guests are rushing through the maze in a panic, and head straight for a door with EMERGENCY EXIT painted on it in luminous paint so it is visible in the dark. Once everyone is out the doors swing shut behind them, and if wanting to be really fancy an exterior sound effect could be added of the door slamming and sealing, which is triggered when the door shuts. This would fill the final gap by suggesting that the facility has been sealed off in an attempt to contain the monster, and prevent further problems.
I'd say they are all fairly simple tweaks which could easily be implemented to fill those final gaps people have mentioned.
I doubt anything more drastic will happen in the lower drop level now, aside from some lighting tweaks, an maybe the odd smoke machine being added, but it does sound like they have continued to improve it during the closure.
So all in all, a big well done to Towers for going back through the ride and improving it. Any improvement can only be positive for Sub-Terra
I believe we have quite a bond lmao). On a brighter note, I'm very happy Towers are listening to reviews of customers and are responding quickly to improve what needs improving. (que the moaning from users saying its not enough and that THEIR little faults with AT should be fixed immediately). But yes hopefully I can be joined by some users in thanking Alton Towers for this gift 
