What problem is this trying to fix that the game has? If you leave a ship without refitting it to a new class for a hundred years, what you have is a very useless ship puttering about. If you constantly refit it into whole new ships over time, you are going to regularly get notified about refits in excess of the cost of a new ship, which always felt to me like you started passing the point where you are replacing whole superstructure and other such things.
Much like how we have 200 year old sailing ships floating around, but if you took one of those and wanted to refit a nuclear reactor and vertical launch systems onto it, your going to pay more than the cost to just build one from scratch, and have to build an entirely new superstructure to support these modern parts.
I also don't want this stepping on my roleplaying. I've regularly played feudal style multi empire games, and its fairly common for a couple of 'pride of' style ships to end up going through many times their normal refit costs just to be a continuation of a legacy starship for nobility or the like. I don't want them doing so only to be told "but it'll break down every two weeks and you can't fix that" even when dropping 150% the price of a new ship on overhauls, and RPing it as the ship being essentially the answer to the ship of Theseus problem. I could just build a new ship with the same name, but then the history is lost, along with the point.
I would not worry about the role-play aspect as you could always put in some extra engineering modules to still make a 150 year old ship work reasonably well for that purpose. I think role-play in this context is a relatively weak argument as you could say that to just about every mechanic that poses some form of restriction in the game. Soon we are down to imagining everything in our heads using that argument...
I think it is important that we can imagine all sort of role-playing environments, so don't get me wrong here...
I still think it is a good idea to somehow force older ships to eventually need to be scraped because of excessive overhaul and refit costs. It is fairly easy to design ships with the intention of continually being able to afford refitting them indefinitely as you do so incrementally over time for very low costs. You can even increase the size of ships just a tiny bit every time so a 9000t ship ends up a 16000t ship after a 100years of continual incremental refit projects.
Now... you don't HAVE to do this as YOU decide if this kind of mechanic should be exploited in this way or not, you also could just scrap old ships and ROLEPLAY it is no longer worth to refit them even if mechanically they still are. I just would like to have a system where I need to deal with the fact that time and usage of (especially military) ships will have unusually high wear and tear as they are built for high stress use and so are also put under allot of stress, even during training exercises. It will ultimately force long term logistical and economical decision makings that is interesting to deal with.
Another thing is experience... as the game really don't model crew rotation and ships need to continually be under training over time it becomes a bit immersion breaking when a ship can retain its high experience and fleet training levels over many centuries with little effort. Perhaps some form of degrading of experience and fleet training over time would be nice as well as ship crews would need to be replace over time as well depending on the service length of the crew which then would effect experience and fleet training levels. You should not have to bother about this logistically... just that depending on your crew service policy ship will need a certain amount of crew and each year the ship would drain your crew pool as old and new crew are rotated from the ship, new and old crew swap places when the ship is at port due to deployment recovery. Only crew from the academies are obviously drained this way and commercial ships should not be able to use academy crews at all anymore if this was implemented.
This would produce some interesting ways that you deal with ship deployment that makes it allot more realistic. It would be very difficult to have ships with many years of deployment without making them VERY expensive in terms of crew cost.
Let's then assume that crew available is more a crew pool in the form of points and not actual numbers. Each ship will then have a service length and a deployment value. Your empire will also have a general service length of crew which are the general level of service length your crew are expected to serve on ship in each term. A ship could never have a deployment longer than its individual service length.
Now each ship that deviate from the empires general service length would have to pay more or less crew points to refill either lost crew or simply to replace them over time. If you lower the service length on the individual length it will require slightly less crew points but more then if the empire general level was reduced to that level. If a ships general service length is higher you will have to spend considerably more crew points to replace crew.
Now... for the more interesting things that also is very realistic. The more incrementally you replace the crew the more they are able to retain their skill and training. Let's say you have an empire wide service requirement of 24 month and a ship with a 6 months deployment rating you will need to replace 25% of the crew after that 6 month is up (abstraction of how it would work in the long term). Now, if the same ship instead had a 12 month deployment rating you would need to replace 50% of it crew after those 12 months in space. In the first case the ship might loose say 9% of its experience and in the second it might loose 25% of its experience (subject to balancing). The reason being that if a ship have more experienced crew they can more easily train the new crew to the higher standard. If you replace all crew you are down to the base experience level and so lost 100% of the ships experience. This also goes for fleet training levels.
This wold make deployment time and actual use of ships even more engaging as the longer they spend in space the more those ship loose in experience once they replace a larger portion of its crew. Obviously the max deployment rate of ships is not the major factor for this, it should always be the actual deployment of the ship, not the max possible. So you can still have a 12 month potential deployment of a ship but rarely use it all to retain experience and fleet training levels better.
Such rules would also put a higher emphasis on a highly skilled base crew or one that you train up with a long service time to retain the skill of the crew easier... sort of quality over quantity strategies.