And here it goes again... Yeah, it's very possible that the Zotaxians and Rock Raiders were going to be enemies (Insectoids are the vehicles, not the aliens themselves), for reasons I'll explain below, but it's hardly proven. The rumor was started when somebody on Lugnet thought he saw Zotaxians in some Rock Raiders concept art (which, if you look at the art, don't really look much like Zotaxians). Then it got blown out of scale and people started saying that, without a doubt, they WERE Zotaxians, meaning that Rock Raiders and Zotaxians must have been enemies at some point in the theme's development. But it's not proven, and never has been, Karl said he isn't aware of them ever being connected at all, I might add. But, there are a lot of similar elements that go for the case as well:
Both themes revolve around a faction getting stranded on an alien planet,
Both themes involve green crystals (though, Energy Crystals are natural resources, Energy Orbs/Voltstones are artificial batteries which collect energy from the planet's core),
Both themes were released around the same era,
Both themes have enemies that are native to the planet which try to attack the heroes,
Both planets are like onions, with many layers and biomes.
So it's not confirmed that the two themes were split early in development, and the original reasoning for the theory is bogus, but there are many similar elements. So it's not proven, but not unlikely. If it were proven that they were originally intended to be one theme, it wouldn't surprise me.