Again, you make a good point and the last thing that any one would want would be for teams and good people to fall away from the game. Regarding this, it would be an issue that would have to be taken under consideration, the example used above only affected two leagues. Some teams may leave that sort of set up and move else where and vice verse.
However, to play devils advocate, the standard is already diluted if you look across the vast majority of leagues. In any restructure, if done correctly, by using as much information available, there should be more competitive leagues and divisions all throughout the country. Promotion and relegation would obviously stay, could look at maximising play off situations. League cups could be changed to divisional cups to cover ceratin divisions, along with on "all league cup" which could possibly mean no team would in any more than 5 competitions - their league, Scottish cup, regional cup,divisional cup and "all league cup"
Again, a lot of waffle from my end, but just my thought on how things could be improved.