When I buy expansions, should I take out duplicate bases?
Each expansion contains functionally unique bases, which makes sense, as every expansion adds a number of new factions, each of which have their designated bases.

Some expansions may also contain reprints of existing bases - in case of Awesome Level 9000, as mentioned on the back of the package (see the image below), there are reprints of the original bases included - likely as replacements of the original cards due to design changes, not to double the chances of those bases appearing in games.



Some ways I could see you otherwise obtaining exact duplicates of original bases is if you bought the same expansion more than once, got a mispackaged edition of the game, bought it used and unordered by the previous owner, or something along those lines.