Parallel Universe can not and has never been able to target immaterial creatures. Period.
Rain of Fire and Plague also do not hit immaterial creatures. The wording is arguably not specific enough, but then again, there is only so much room on a card to describe what it does. (Adrenaline has an entire article about it describing its mechanics, for example.) This is assumed to be intended behavior, as Zanz hasn't said a word about them in the five updates he has issued in the past three months. Immaterial status makes creatures very hard to deal with, but it isn't overpowered. Elements is not M:tG, so immaterial status has different implications than the shroud status, regardless of the similarities. In the future, who knows... maybe there will be a global effect that kills all creatures regardless of status. Until then, just kill your opponent before his immaterial creatures kill you.