Ah yes, Alpha's Sigma Lightning attack. Dance, baby, dance! Or just use an Invis chip or something else that makes you immune to it.
Of course, having both versions of the game can work to your benefit. I know I played an awful lot through Blue before I really touched White. Thing to do? Trade a bunch of powerful stuff over that you normally wouldn't have access to yet. Alpha is annoying normally but if you throw up a Life Aura he can't touch you with anything. Ha!
Still, I think the cheapest attack by far in the alternate timeline games is Pegasus SP's giant Iceberg of doom. Absolutely undodegable and unblockable. Only way to avoid it is to get lucky and be able to throw up an Invis, Barrier, or Aura in time. And unlike Leo and Dragon's ultimate attacks, which you can just absorb the damage from if you're doing well enough, Pegasus' freezes you, meaning if you get hit by it, you also get hit by his next attack. So even if you can survive it, you're still probably toast if you get hit with it. Much annoyance. Pegasus remains the only boss (Well, except Andromeda) in that game that I haven't S ranked. Thank goodness for cipher mail so you don't need to!