I agree it is difficult but not impossible. It really depends upon what you want to do.
For example, one "bug" which has been fixed in the original WPC code is the random skill shot award for BSD. This is known to be problematic for tournament play and a new ROM was created which capped the award at 500k - http://papa.org/learning-center/director-resources/directors/game-notes/#B. As you can see PAPA encourages the use of this ROM for competition.
What you're suggesting for RS is much more significant because it involves a change in the rules. The game requires you to drive from east to west and then repeat. Randomizing this could be done to some degree within the existing rules but given how cities are changed with shots to the pops, there seems little point. So if you wanted new rules on the existing hardware, using something like FreeWPC would be the way to go. But this is not trivial either - look at the 2000 hours James Cardona put into his Demolition Time code - http://pavlovpinball.com/completing-the-code/
Doing non-WPC machines is even more difficult. WPC code is well-documented and well-known. Not so much for machines like JP. ChadH did an update to DESW which involved working through the assembly code in PinMAME and has done the same thing for JP, which many hope will be released soon. The PinMAME route is another option but this is very hardcore and likely would take thousands of hours and a thorough knowledge of assembly coding.
Then there is the suggestion for using something like P-ROC. This is probably the easiest route to go in creating a new ruleset but also require investment in new hardware and it would be difficult to get many people to use it since it would require them to install P-ROC hardware in their machines.
There are other issues like copyright, IP, test and validation to name a few. If it were easy we would have seen updates to a lot of machines by now. Heck even Rick @ PPS asked for bugs people would like to see fixed in WPC code well over a year ago and to the best of my knowledge, the holder of the original source code has yet to release anything new in that regard. That should tell you how hard it is.