>>Just like in real life, the good skippers would get the perks.
Not always. Truth be told, the current implentation is arguably the most realistic. Yes you'll get your back scratched if you have a good rep, but thats not always how logistics works. And if your sub gets a refit, is all about logistics.
For the most part, pearl boats had to go back to mare island, san francisco to get a refit. Boats based in austrila, i have no idea. Its a matter of having the materials and facilties available in order to do the refit to begin with. That and real world needs. Say for example a sub was really badly busted up and needed to dry dock. They might decide to do the refit right then and there since she boats laid up already. Doesn't matter if the skipper is successful or not, the boat needs to be repaired, and it only makes sense to refit it while its out of service.
This link is intresting:
http://www.shipcamouflage.com/submarines.htm
Note that " MS 9" is the black paintjob, and "MS 32" is the grey paintjob. If you click on the sub types, notice the year in which these were done.