It's both a complaint and a point of interest, to me. On the one hand, it really sucks that our heroes really are stuck fighting an unbeatable foe. When I had Valerian say that it really didn't matter what Rael could do and if he knew, the first thought that crossed my mind, as a player, is 'he probably has the whole Twilight permanently divined - he knows where we are and we stand out as a point of nondetection, so he just doesn't care about us yet', which is a really, really depressing and lame thought because it means we literally can't win unless Rael screws up. If we get the Vengatol and it doesn't have enough juice to start playing with some fundamental forces (or if Burson escapes with it), we're completely screwed. I have a plan set already if the Vengatol is as primally powerful as it sounds like it is, but otherwise we're completely in the dark.
On the other hand, there's something to be said about fighting a nigh-unbeatable foe. It gives the story a very Black Company or Myth kind of feel, where the good guys mostly eke out minor victories as darkness wins and wins, until a brilliant gambit wins the day for the forces of good. And when (not if) we beat Rael, our victory will be absolutely sweet because we will have defeated an effectively unbeatable foe. Personally, I feel that unless we have something that lets us proactively fight Rael and start screwing with him directly, I'd rather stick to sidequesting and accruing power, character development, and more evil misfits for the ship. Our crew is already so interesting that I could spend a whole session just chatting with them and having minor adventures, and each PC has his own minor goals that have been calling for attention for a while and we haven't been able to tackle (Valerian seriously wants to return home, it's just that we've had literally no time to rest so far). We don't need an epic plot that is totally out of our league when we can have a super engrossing plot that is smaller and more character-focused.
PS: As for a complaint of my own, the only thing that I really don't like is the fourth-wall breakingness and obvious referencing. It's funny if limited to comic relief characters and the occasional joke, but when I see Rael make a quip directly at us just as he's slouching in his throne and monologuing, it breaks my immersion, which is really bad when the story is generally very engrossing otherwise. I'd cut down drastically on the mention of classes, levels and such, and just use in-world terms. It makes the world feel more alive, instead of being a setpiece for our antics.
PPS: On the plus side, the thing I really DO like is how the world has adapted to our actions so much - Valerian started the game by saving Raita, and through persistence and kindness made her turn a new leaf. He spoke to Tevaline and slowly started to cut through that aloof shell. He refused to let someone die on his watch and I got a chance to jab Tevaline out of killing herself instead of getting cutscene'd into a death. It's very cool stuff, and I love it.
PPPS: I'll get character rankings up later today. Additionally, I'll see if I can get logs of our conversations up for easy perusal.
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Twostuck, Homestuck RPG: http://www.gamefaqs.com/boards/8-gamefaqs-contests/62168402