Note that the Ancients as presented by the canon texts were never intended as limits for your games. I'm continually astounded when I read about people feeling limited by the OTU because something isn't in the canon texts. It's YOUR GAME, you can add elements.
"It's YOUR GAME"
This is something that I think way to many people who play RPGs seem to forget. It doesn't matter if you are playing Traveller, D&D, Star Wars, Pathfinder, or any of the other 3 million RPG games out there the bottom line is that the moment someone decides "I am going to run a game..." they have essentially created a "pocket universe" that is all theirs to do with as they will.
The settings that any of these games provide (including the races, classes/careers, skills, worlds, items, etc) are all just starting points, seeds, and guides to help the GM get started. To provide a general frame of reference. As the GM (and to a lesser extent a player) you have complete control.
You don't like the way Jump drives are in Traveller, so make them hyperspace drives. Not a big deal. Hate that laser rifles require a backpack to power them? *poof* now they are like blasters in Star Wars with tiny battery packs or weapons in Mass Effect which are limited by heat generation. Want elves in space, done. Instant galaxy wide communications, sure thing. IT IS YOUR UNIVERSE, PLAY GOD!
The only impact these decisions really have is when you want to incorporate materials or adventures that were written for the "official" universe of whatever game you are playing. You may need to adjust things as you go depending upon what changes you have made to your universe. But since you already made those changes, it shouldn't be an issue.
All that said, the benefit of sticking to canon is that what you create can easily be shared with others if you so wish.