The universe is getting big...

How to add more new creatures without screwing up existing ones?

 

I think you've answered it yourself in the first sentence of the paragraph: UNIVERSE IS ... BIG.

Step one: Make the galactic map BIG. Like really BIG. Maybe not No Man's Sky big, but pretty big.

Step two: Add new creatures to the outside of main campaign realm. Make Magellan unable to travel there by fuel/distance limitation.

Step three: DLCs will upgrade Magellan to be able to safely travel further outside to see and meet NEW THINGS. Who wants to fool around in the same space anyway, right?..

*The stars only represents the in-game density on a galaxy map and not the quantity.

**The map is round, border-less.

 

This will keep exploration desirable, all creatures will be new and fresh. You might also add a bit more planet types there too... Win/Win situation in my estimation.