Yes, the Covenant are an excellent example of what I was thinking - well done for considering that first! Another example that would be good - especially with the dimension-hopping aspect, and the idea of co-opting and 'adapting' the races and their technology as they encounter them - are the [url=http://half-life.wikia.com/wiki/Combine]Combine from Half-Life 2.[/url] I especially like them as they're very imposing and they manipulate their 'subjects' genetically to create more creatures and species for their own forces, as well as manipulating and enslaving the rest of the population to further their own goals. I like the fact that a lot about them is unknown, and you never really get a true scope for what you're dealing with, and it's almost like some kind of monolithic giant machine, where the working parts just happen to be organic species and people. 
That can dovetail nicely with the idea you have about their having psychic abilities and increasing intelligence and knowledge as the ranks increase, as they need more information and ability to effectively deal with controlling more forces and having more 'access' to the larger base of knowledge and resources at higher levels. 

I'm glad you agree about character sheets too - it's useful to have a bit of reference material sometimes when you want to check something in a hurry, and as you say to collect thoughts. I'll get one up tomorrow, if that's okay?