Fair point - I agree that clubs playing through all teams is great when it is workable. Unfortunately first teams can reach the same level in a variety of ways:
Take the community club picking local amateurs - the structure of the club has created a strong 1st team and therefore the 2nd and 3rd teams are likely to be strong as well, everyone would like to think this is their club, but we all tend to look in the mirror through rose tinted spectacles.
Compare this to the club with a fully paid first team - often this means a squad of 25 paid players with little opportunity for others to get into the first team - these clubs often have a lack of opportunity for inexperienced players and replace player development with buying players in, they can at times struggle to even put out a second team.
The truth is that most clubs fall somewhere between these two stools, but moving up the leagues the difference between the two becomes more extreme (e.g. Sheffield Tigers could not put out a 2nd team this season). Therefore the number of times that clubs with comparable first teams have well matched second teams becomes less and less. Its great if Selby can go to York and have 4 good games, but it is not sustainable if the second team were in one sided games every week.
In theory the merit tables should address this issue and despite their faults I think that the organisers have been sensible to split the league after Christmas to provide more competitive fixtures. The calendar also provides a number of blank weeks to play other friendlies. I don't think there is a perfect system and the days of players committing to Rugby for 35 weeks every winter are behind us, personally I am just pleased that as many players as possible are getting regular competitive games, but success in the merit table may serve as additional motivation to some.
I would also add that if Selby (and others) committed to the merit tables it could increase the level of competition and strengthen the competition, which is ultimately of benefit to the first team as players are gaining experience in a stronger standard of rugby.