Wormhole in Cathedral
While I was mapping out that level I felt that I needed to do something a little different than the main campaign. I tried to bring attention to the hole by its placement in the room in hopes that players would use it. However, I can see how it's not the most intuitive design decision. I think I'll see how a whirlpool particle effect looks and do a better job of teaching the player how it works.
A different graphic would also do the trick. Something that doesn't say "I'm dangerous, avoid me" so players don't, um, avoid it as a matter of course.
Speech Bubbles
I was confused as to whether you're against the speech bubbles entirely? An orphaned speech bubble would certainly be funny but I'll prevent the Scout from being affected by the rock.
The speech bubbles are fine. I was just commenting that, as a consequence of the speech bubbles, everyone you can talk to has to remain stationary. No biggie.
Action Offstage/Difficulty
How could I improve this? My initial thought was that Vanilla Aquaria was more about discovery and so the same type of exploration in Sacrifice is not satisfactory. Should I add more "story purpose" to what Elena is doing? Would more boss fights be a remedy to this situation? On the subject of difficulty is there an obvious factor? Are there to many save crystals to replenish health and/or to many opportunities for food items? Is it case where knowing all enemy and boss patterns removes that initial difficult feeling? I've had someone tell me they thought it was to hard and where I can't please everyone it seems that the majority think things are to easy.
That's interesting, because it seems to me that Sacrifice *is* about discovery and exploration. The problem is that while Elena is off discovering things about her past, the main plot is moving on without her. Fixing this would probably take more work than it's worth - as I said, video games can get away with this sort of thing because the gameplay works on its own.
If you're looking for a quick fix, though, there may be a way to do it. Look for ways to make the player feel like they're participating in the main storyline, and that the things they do cause other things to happen. To give more specific suggestions, I'm afraid I'd have to play through again.
As for difficulty...hmm. It's not the save crystals or the food items. It's not the bosses either (actually, with three exceptions I found the bosses in Aquaria to be fairly easy). The main difficulty in the main game came through just swimming around in dangerous waters. In Sacrifice, you can in large measure just ignore the enemies if you want to. Try that in the southern "open waters" of the main game, with all the projectiles and nautiluses, and you won't last very long at all.
Young Fred's Brain
I've been brainstorming a level that was cut and added numerous times during production in the Veil (door with no holder blocking northeast).
Oh, so *that's* what that was for. You had to know that, after talking to Young Fred, we'd go moving every rock we could, right?

Lastly, FYI, my last save game clocks in at 5:30. I probably spent 30 minutes in the ending sequence as well.