I just don't understand why you believe that 50 seat airplanes are inefficient. Show me some numbers that will prove a 737 is cheaper than an RJ.
As you touch on further in your post, cost (or efficiency) means a couple of things - usually contradicting each other.
First, there is CASM, the metric used across the industry to compare airlines cost structures - how much does it cost airline A to move 1 seat 1 mile? Is that more or less than it is for airline B? In general, barring advances in technology, the more seats an airplane has the lower it's CASM. Not always 100% accurate for a number of reasons, but a good rule of thumb.
Second, there's segment cost - how much does it cost to fly airplane X from A to B and is it more or less than flying airplane Y from A to B. In general, the smaller and slower the plane the lower the segment cost.
Rule of thumb 1 (ROT1) says that everyone should fly the biggest planes they can get - eliminate everything smaller. ROT2 says that everyone should fly the smallest planes they can get - every segment would be flown at very low cost. Obviously you can't do both at the same time, so....
That is when the market being served comes into play. There's not enough traffic every day between AVL and CLT to justify flying 777's between the two - no matter how low the CASM may be you end up paying to move an awful lot of seats you can't sell so why pay to move those extra seats. So you use a 50 or 70 seat RJ. It costs more to move each seat, but it costs less to fly from AVL to CLT (segment cost) because there's a lot fewer seats plus you sell most of the seats so don't pay to move a lot of empty seats. In other words, you use the plane with the lowest segment cost that will carry the people that want to fly that segment.
On the other hand, you don't use a CRJ-200 for PHL-LHR even though the segment cost would be lower than using an A330. Using the RJ means leaving people behind because there weren't enough seats to sell, which means lower revenues. And who going to want to make 3-4-5 fuel stops on the way - you'd end up flying empty CRJ-200's to LHR.
In other words, there isn't a single perfect airplane for all markets. So network carriers use a variety of airplane types and do the best they can to match the airplane to the market - using the smallest plane the market will support to lower segment cost while at the same time using the biggest plane that the market will support to lower CASM. Then you have to throw the mission into the equation - primarily by using airplane that have the range to fly between the cities you want to serve with non-stop service.
What's hurting the 50-seaters is the price of fuel. US Express, taken all together, has a CASM of ~23 cents last year - it cost ~23 cents to move each Express seat 1 mile. Since that's the average for all the Express fleet, from under 50 seats to 80-some seats, the 50-seat RJ probably have a CASM over 25-30 cents. That CASM has to be covered by revenue, so enough people have to pay enough for their ticket to cover that CASM for whatever portion of their itinerary it involves. For comparison, mainline has a CASM of ~13 cents. So the cost of fuel is driving up the CASM and segment costs of the small RJ's faster than the bigger planes which have more seats to spread the extra cost over. So someone going AVL-CLT-LGW would be on an RJ to CLT (the lowest cost way to fly them), then get on an A330 to LGW (the lowest cost way to fly them on that segment).
Jim