To be honest, the 2nd effort (Red Rock-based) appears to be the better. In this latest plan, I'm not sure what you are trying to gain operationally with the extra loop. Is it intended to be a twice-around or 2 normally separate loops? The object of twice-arounds in small layouts (and yes, 6x6 in N is still on the small side) is to gain a longer run and the capacity for longer trains. The cost is loss of sincerity - the same train passes through the same scene twice, but on different tracks. If over-under is used, much of the distance is spent on a grade, requiring special arrangements to do switching - uncoupling part of the train causes it to roll away.
The yard, as drawn in your last plan, is not particularly functional. Classification yard design is discussed quite well at
http://www.housatonicrr.com/yard_des.html. At it's very basic, a yard that is more than train storage needs the following:
- a train length long arrival/departure track so trains arriving/departing in either direction can couple/uncouple their road power. This means either a passing siding or an escape crossover to get the road power out of the way. Using the main as the arrival/departure track ties up the main for great lengths of time - nothing can use the main while a train is being built or taken apart.
- a yard lead or drill track at least 1/2 a train length long. This is where the yard switcher pulls a cut of cars from/to the arrival/departure track. Again, if the main is used as the drill track, it is tied up by the yard switcher.
- 2 or more classification tracks. These are your typical yard tracks. They should be at least 1/2 a train length long (preferably a whole train length, along with the drill track) to make life reasonable for the yard switcher.
- On a continuous run track plan, not blocking the main with yard operations is a big deal. On a plan where the track ends at the yard and with possibly just one operator, the yard can be simpler. There is only one direction of arrival and departure to design for. Blocking the main might be such a big deal, since the train is to be broken up, and a new one put together before departure anyway. This would be particularly true for modeling branch or short line operations.
In the last plan, industrial spur tracks seem to be scattered like confetti. In the real world, industry is generally clustered around towns, with miles of single track linking the towns. Mines are the big exception, but for modern mines requiring rail service, a single spur doesn't cut it. A mine needs to output cuts of car loads a day to justify itself and rail service.
The main problem with the 2nd (Red Rock-based) is that the center pit is too small. Even though you are young and skinny now, it doesn't mean the pit is big enough to share with anybody else. Even turning around in a pit with a 24" dimension will not be comfortable for most people. 3ft by 3ft is the minimum pit you should consider (for one person!). Set up some cardboard boxes at chest height to verify what I am saying.
Also, unless there is access on the outside, reaching more than 24" on a chest-high layout requires a step stool. The step can extend one's reach to between 30 and 36", but that's it.
Finally the place where you duck under to enter the pit should be as narrow as you can make it (preferably 12" or so). The wider the duck under is, the more likely you are to have a sore head, scraped back, and magnitude 9 earthquakes on your layout.
These are my thoughts, and your choices.