The principal difference between the ISR and the RPI is that the ISR is not subject to the same connectivity issues that plagues the RPI. This is because the ISR employs a real algorithm that is recursive in nature and extends far beyond two levels deep into SOS (OWP and OOWP).
From Boyd's page ...
"The basic idea is an iterative one. Begin with all teams set to an even rating -- 100 in this case. Then, for each game played, give each team the value of their opponent's rating plus or minus a factor for winning or losing the game -- 25 in this case. Total all of a team's results, divide by the number of games played, and that's the end of a cycle. Then use those numbers as the start of the next cycle until you get the same results for each team for two consecutive cycles."
This is the best I can explain it without coding the algorithm for you. But simply imagine an RPI with no limits (until the recursive stop condition is hit) as to the depths that SOS is calculated. Meanwhile, RPI has an arbitrary depth of two (OWP and OOWP). Imagine OWP, OOWP, OOOWP, OOOOWP, ... until the stop condition is hit.
The only knock I have against the ISR is that it does not take into account home vs. road games. But that was not its intent. It was intended to provide a better version of what the RPI was attempting to accomplish.
As far as "upgrading" the RPI if I was stuck using it ... I would equally weight win/loss percentage and strength of schedule. I would also apply a factor to home wins and road wins. I have not decided what that should be. But obviously a home win would be worth less than 1.0 and a road win would be worth more than 1.0.
But again, the above is simply patching a flawed system. You cannot accurately assess SOS by simply going two levels deep. It is an arbitrary system.
Brian