1 - I think you're proving the point. Some think it's worth it to sit on teams in a certain league, or even join terrible teams in a certain league, rather than spend the time on a successful team in another league. Neither choice is wrong, but there are some pretty clear drawbacks to either.
2 - Geography (for practices) plays a point, but affluence matters more as at some point the costs are more about ongoing travel for most games and tournaments - not only the player, but anyone who wants to watch or participate. Four Seasons only runs hotels in the priciest cities, and isn't sued because they don't serve low-income areas (other than licensing their name to landscaping firms who put on presidential press conferences). The map overlaying richer areas makes sense - and it's where anyone starting or running a league for club/travel soccer would probably concentrate on.
3 - Of course there are exceptions to every rule - but the fact that we have to list the clubs that aren't able to join the top leagues pretty much seals it, doesn't it? Sure - there are some examples like Tudela, SoCal Elite, or some others that might be strong additions to MLS N or ECNL, but there aren't a ton of well-run, successful clubs with strong coaches/DOCs/players that for whatever reason are languishing in leagues below their stature. Team based pro/rel would fix this entirely, but it probably isn't a large enough problem to warrant that solution.