Sure you can; you can also add your own areas, events etc.
I've only ever changed the scripting of existing enemies, but this should be all you need to do to add your own new enemies:
1) Decompile 
script.rpyc (and delete the original file):
	
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2) Add your new enemy to 
scripts.rpy; the minimum is:
default mynewenemy = [...]
Add to 
default enemies = (mynewenemy, ...)
Set 
default persistent.MyNewEnemy = 0
Add to 
default temp_defeated_enemy = {"MyNewEnemy": 0, ...}
3) Extract 
archive.rpa (and then delete the original file):
	
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4) Add your images to 
\images\Enemies\MyNewEnemy .
5) Write your own 
MyNewEnemy.rpy, referencing any new images/audio (you can use any other enemie's rpy as basis after decompiling).
IMPORTANT: Remember, that any rpy will automatically be compiled into an rpyc when running the game.
OPTIONAL:
A) Extract and mod 
screens.rpyc for the Enemy Info Screen:
Add a block following 
if persistent.MyNewEnemy >= 1:
It's easiest to just add it last to its respective area; make sure to add to the X and Y coordinates accordingly.
B) Extract and mod 
Main\acheivements.rpyc (sic!), if you added a new one via 
MyNewEnemy.rpy .
C) Add new sounds to 
\audio, that you might have referenced in 
MyNewEnemy.rpy .