Require these be powered by the alien artifacts. This would go hand in hand with the "Alien-Fuel" mod. That way, one cannot sit back and simply work up to replicating items with ease.

In an earlier version their was a liquid which was needed to replicate stuff. As I updated the mod I deleted everything which wasnt really needed. At the moment i dont want to reimplement it. Maybe later :)
If you dont want it to be too easy then play around with the config options.
replcator_base_power = 1
replcator_power_factor = 3.5
This will make the later tiers highly inefficient: Tier 5 has (3.5/2)^-5=6.1% efficiency of the tier 1 replicator.
I thought about an option to change how th recipes proportions a distributed to the replication tiers. At the moment its 1:1:1:1:1
Then yo could change it to 1:2:3:4:5 this would make it harder to replicate more complicated stuff.