I like Number 2 better personally, but in-game Lucca's face and "Final Mix" get covered up a little. Number 1, with Lavos, fits in beautifully, though, and I really pushed photoshop to give some pretty colors for the crab nebula behind him there.
What I'd recommend, is that you use Number 1 for the actual game opening screen, and then Number 2 to replace the screen at :35sec in your video. That way both get used, and It's almost like a story. Lavos floats around in space, til the Team leaps off Earth to get him!
The "logo" I used is a combination of the "Chrono" from Chrono Resurrection, photoshop texture and stroke, and some crafty text to make a fitting "Alter". I tried to make it look... altered.
I'll make a few for CT2 also if you want.