I apologise if this has been brought up before, but would it be feasible to implement a system where commanders also have a chance of losing efficiency bonuses once they reach a certain time in service?
I tend to treat my civilian administrators as abstractions of an entire government apparatus, and hence I assume the efficiency bonuses are tied not to a particular leader but rather to the entire colonial administration of thousands of civil servants. I find this better from a RP perspective because this leads to certain colonies being better than others at certain functions (which I RP as resulting from local expertise, incentives, and infrastructure), hence my colonies feel more real and unique. And it sometimes forces me to make sub-optimal decisions - like building up a new naval base not at the local warp point nexus, but one system over at a colony which is actually good at shipbuilding.
The problem, of course, is that immortal (story character) leaders tend to universally end up with sky-high bonuses of everything. I've been solving this by periodically randomising leader bonuses, but this gets tedious as the game progresses and I would really like an alternative. Essentially, past a certain time in service (say 20 years), I'd like to have commanders start rolling for a small reduction in their bonuses in addition to the usual rolls for an increase. Does this seem reasonable?
There is an East-West split in that assumption, Eastern cultures (China, Japan, Korea, Vietnam, etc.) place a high value on the elder members of society, deferring to their wisdom, moral authority, etc. In the West, older people are seen as less capable, out of touch, etc.
Partly that is because as you get older, your perspective changes (based on a lot more experience of life) and you value different things (time vs money for example). Younger people generally don't have the same frame of reference (less life experience) so they can't understand that different perspective. In the East, that is understood and the elders are consulted for their hard-earned wisdom. In the West, they just assume older people are 'out of touch'.
So, apart from actual age-related diseases that impair mental faculties, which is covered by the medical conditions in Aurora, I don't subscribe to the Western 'older people are less capable' paradigm. I am certainly far more capable and wise than I was at half my current age, because I have twice the life experience and I have learned from twice as many mistakes

I realise that in your above suggestion, you reference 'story characters' that can't get ill, but being extremely capable is the whole point of story characters.