difficult question and can't be easily answered by one person or by one method couple of ways to do it exist but i couldn't think of them off the top of my head
core idea would be giving more ways for marines to punish people for disobeying but that's more grief tools, or offering more incentives to do things - adding map objectives and things to secure that aren't as painful as static communications. engineering is one way for instance such as allowing you to maintain power and giving you a passive benefit (lighting)
colony blackbox in its introduction was also a good idea since even though it was just a roleplay item people interacted with it and tried to work around it. IO's are also a good method of this since it encourages exploring more of the map.
for xenomorphs enabling different stratagems to function more by giving them options (it could be interesting for instance to have different hive types that could be selected that are specialized in certain ways but people will find a meta around this) or by reducing their overall building speed (so they don't shit out 30 million walls and shit) but making it harder to easily clear these areas. if you've seen xenos build out of caves, even with proper CAS it still has a proper threat - it offers them more cover that has to be cleared and reduces marines lategame power, but few bother to do it presently
another possible method could be positive reinforcement of doing unconventional things - positive notes or reinforcement about it from staff at least shows that somebody appreciated it. i also feel this could extend to roleplay - new players and many players want to RP but feel ostracized and similar since it feels like nobody feeds back on them so they don't initiate. positive reinforcement on both of these instances could help to an extent