I finished the game in about 5 hours, in a single session, with only small breaks.
First I played through Shays part completely, too excited on what happens next to even consider switching to Vella. I did not make the connection between the two parts right until the end. For a short moment I thought that Shay could be Dead Eye, yet I abandoned this idea rather fast. Well, when I finally had that damn Mog shot down, and the characters change location, all the hints started to connect. It was already after midnight (how could I stop playing when the story is so thrilling?) and my mind had already slowed down quite a bit at that a late hour, so the realisation of the many links between the two perspectives was dripping only slowly into my consciousness, bit by bit. It was at least five minutes after that final scene that I fully realized that the pictograms of the creatures Shay rescued resembled the costumes of the maidens ;-)
Thanks, people at Double Fine, for that great first act! I really enjoyed it very much! The beautiful artwork, the thrilling story, the excellent voice acting, the epic music - it all worked together like the components of a rather complex machine that altogether just works perfectly. I'm really looking forward to the second act!
The game might seem a little bit short, but consider, that up to now it's approximately the first half. I've been counting scenes here and my rough estimation is, that it will in the end be comparable in size to Loom. The game was relatively easy (as was Loom, a long time ago ^^). I only got stuck once for a short period of time with the Riddle of Yorn (everyone who didn't yet: ask Curtis about it!), yet everything made sense, as soon as I saw the tree once more. For me, the difficulty nevertheless was OK, since the story needs a certain tempo to work, and making the game more difficult might slow the player down too much for the twist to have that jaw dropping effect.
Coming to wild speculation, I agree with Jay Tholen (Post 82) regarding the simulated space, and with android (Post 96) that there is no real vacuum "outside" the ship. I also came to the conclusion that Mother might be a life woman, just as Klink wrote in Post 105, yet to me it never appeared that she might in fact be his real, organic mother... I agree with FlamingFirewire (Post 106) that the maidens Shay abducted might be possible brides. (It's kind of frustrating to post so late, since nearly everything I wanted to say has been posted already...)
I also have thought about the, in my opinion, lower difficulty of Shays part compared Vellas part. Could this be another hint that all he experiences is actually set up for him? I mean, if Marek is part of the Mother-Ships game, Mother herself would not put obstacles in Shays way that he cannot solve rather easily.
@mmikkel: I think that "lowering the shields" translates to "opening the mouth".