Early in the game command points are somewhat useful. The penalties for using them are a bit steep and ambiguous (are they permanent and cumulative or do they expire? Who knows, the game doesn’t tell us)

By mid game the command points are essentially worthless and certainly so by late game.  I have thousands of unspent command points - and literally nothing worth the time to spend them.  Like seriously - 50 points given when I ‘inspire’ my scientists when the item I am researching is thousands?

my suggestion is to modify the command purchases as follows;

1) Update the description to include when negative effects expire - if at all. 
2) Reconsider the cool down periods.  I get it - the cool down is to prevent spamming - but isn’t that also the point of the negative effects as well as  the point cost?   Pick one.  Just one.
2) Scale the effect (where appropriate) so that mid game, instead of a worthless 50 point bump I am getting a worthwhile bump - either remove the cooldown so I can stack the benefits or  compound the benefit; like 50 tech points + x% more per use (with the cost scaling up as well, like culture points do.)

Do that and I may decide to build a starbase next to a command artifact.  For now though it is a worthless gesture.