Now -- what are you listening to? V3

This is indeed better, as is perhaps every Ayreon album except maybe Actual Fantasy, but I can't think of Transitus as a letdown. It's just different. And I think that's OK. 

The Source has tons of singers in the same track most of the time, but Transitus keeps things much simpler. If we discount Baker's narration and Bovio/Westendorp as backing singers (same with all the Villagers) the most lead vocalists on any track here on Transitus is three, which is very restrained for modern Ayreon. Discounting the final song on The Source, three is the least amount of singers in the same song. 

I suppose you could say that Theory of Everything was also like that for its actual tracks, but the 20 minute suites in full used at least five of the seven. And all Ayreon albums except for TFE, AF, TDS and FotM all had songs that used considerable more than three singers in one song, even if they also had tracks with one or two at most. 

So I think if you go into Transitus expecting more of that you may come away disappointed. I'm not suggesting that's how you personally feel Travis, but it is something I wonder about when I see people complaining this one is not enough like The Source. Personally one of the things I like the most about it is that he did not rehash his other recent albums. This is a very unique record in his whole discography. I like it more with every listen. 

It really doesn't though. 

Okay, so there's one part that in the actual music that is really unclear without the comic and that's Lavinia's role in the event of disc 1. Lavinia is a medium and she gets a vision of Daniel's death in the fire and misunderstands what Abby was telling her father, thinking Abby murdered Daniel. This happens in track 1, in the comic panels. For some reason this is completely ignored in the actual music though, which is weird. 

It's this event that sets up Lavinia's actions on disc 2, as she feels like she is haunted by Daniel's ghost and turns to Henry, who she knows was always against Daniel and Abby being together. Henry further manipulates her, because that's the kind of guy Henry is. Henry's character is very firmly established on disc 1, which allows his part on disc 2 to make sense. Despite everything he did against him, Henry did love Daniel (whereas he seems to have been dead to his father for choosing Abby, which is probably why the father never appears again even at the funeral). Henry is not a good guy though, and is looking for someone to blame: Abby. And Lavinia, in her mistaken belief, gives him further cause to take action, which he does through manipulating her. 
 

Most of disc 1 either takes place in Transitus, the place between this world and the next, which is where Daniel actually is through the story since he dies in track 1 or are a flashback, which establish the background for the events of disc 2: why Henry is so against Abby and why Daniel needs to save Abby.

Disc 2 then takes three paths to its conclusion: Henry and Lavinia's plotting (Daniel's Funeral, Henry's Plot, Message from Beyond), Daniel trying to save Abby (Hopelessly Slipping Away, Daniel's Vision, She is Innocent), and what the Angel thinks about it all (This Human Equation). After Daniel is able to use Lavinia's ability as a medium to get a proper message to the world of the living (having previous failed to do more than have Abby and presumably other characters feel his presence - Henry claims to have, but we don't see/hear this, leaving it up to interpretation whether he really did or was just part of his manipulation of Lavinia), Lavinia realises what she'd done and runs to Abraham, who unfortunately is too late to stop Abby from committing suicide, just as Lavinia had suggested Daniel wanted. His rescue attempt results in his own death, again witnesses by Lavinia through her power, which causes her to fall down the stairs are die, which the implication being that the Angel sends her to hell, not willing to hear her excuses because in the end Lavinia was tempted by the prospect of the inheritance that her husband Abraham would get if Abby were to also die. 

Ultimately the story has a happy end with Daniel and Abby reuniting in Transitus and moving on to the next life together. I presume that Abraham also went to heaven rather than hell, but he's never shown in Transitus, unfortunately. In an epilogue page of the comic, not on the album for some reason, Henry is shown about to go to hell. 

The Transitus scenes in the comic have some symbolism if you look carefully at certain panels: those wearing white are heaven bound - black are going to hell. And this seems to be an internal judgement by oneself thing because Abby in in black all the way up to reuniting with Daniel and realising that she wasn't to blame (because she was blaming herself), then she's suddenly wearing white. 

I'm not saying that the story doesn't have problems from certain points of view. There's a lot we don't hear (but then we don't really need songs covering a whole week of Daniel trying to save Abby from beyond the grave) and it does rely on the comic an awful lot, but the story does make sense. At least as much as a story like this is supposed to make sense. And disc 2 definitely doesn't ignore disc 1. You've just got to interpret it right: in terms of a linear narrative, Condemned Without a Trial directly follows Fatum Horrificum. 

I hope that helps.