They are lame a lot of the time, but still funny 99% of the time, it's like a guilty pleasure.
Blazblue is one of the very few games to get me to laugh, out loud, more than once a playthrough, I'd be pretty sad if they got rid of the joke endings.
As far as hopes regarding the new story mode, I'd like see three things...
A) End the current storyline, doesn't have to mean the end of Blazblue and future stories, just the whole 'fighting the Library and Hazama and the Imperator' story. I'm afraid if they continue for too long, it'll end abruptly for some reason, either because they can't or won't make new Blazblue games, and we'll be stuck with "To be continued!" forever. Go ahead and have new plots in games that come after CronoPhantasm, but don't drag this out like a Dragon Ball Z arc.
B) Change the format of the story mode from what it is currently, where you pick one character and follow that character around until an ending occurs. I'm not saying GET RID OF IT COMPLETELY, what I'm saying is, don't make it the bulk of the story mode.
The ending of Continuum Shift suggests everyone is going to be in groups, to a point, you got Ragna and Tao, Noel and Makoto, etc etc (I don't remember exactly what the group compositions were, but practically everyone was a part of one), it would be silly for everyone to get to Ikaruga then suddenly WHOOPS WE ALL SPLIT UP FOR A BUNCH OF REASONS.
C) Bring back Teach Me Miss Litchi, regardless of what's going on with her now, and Help Dr. Kokonoe too, heck introduce a new thing while you're at it too. These little animated sessions were my favorite part of both games.