I think that's a basic flaw in your view of the "system." Any overview is going to fall short but as I see it (on this limited point only): his system is to develop a player to be productive within his framework, however long it takes. In the past this has probably ranged from a few months of practice and a half-dozen games to most of a first season to two seasons (maybe the norm) to four years to never. Many of the players who never completely got it were still major contributors and starters for years.
Looking at a theoretical four year process you are exaggerating the effect of changes such as transfers and pro-exits. If the pressures from those factors increase it dos not necessarily need to impact the way Geno works. He's still looking for his kind of raw characteristics, he's still helping that individual player develop as fast as she can, he's still (in games) using the best combination of those players he has at hand. On this limited point you raise, nothing really needs to change.
Okay let's look at my very simple understanding of the system...
It is generally expected that the rookie year in the UConn system is the toughest year, true?
it is of my opinion this is the case for a few basic reasons 1) the learning curve of all the options of the read and react system, 2) the difference in Pace of the game from HS to College, and 3) Coach has a tendency of breaking down his star players especially, highlighting some of the things they need to improve upon
The sophomore season is typically when the coaching staff is hoping to see a leap in confidence and productivity as the players have now a better understanding of what is expected, all while continually working on becoming stronger, healthier, Smarter. This is also a stage where they're typically challenged to contribute in other areas they are not comfortable with.
Junior Year, by now everything should be habitual, from practice regimen to game preparation and execution. Continued growth as a player and teammate. Continued development of other aspects of the game, where possible.
Senior season, The biggest adjustment is learning how to be a leader...
that is the basics of the UConn system, by default things such as learning to speak to the media etc, comes with the territory due to the exposure the programs receives.
So if a player leaves before completing all four years they will technically miss out on an important aspect of the UConn process. Though there are some exceptions to this from team to team.