We've always had good luck with the buses at CSR, but I've read the same reports you have. Sometimes you just have good luck and sometimes you don't. It's that way at any resort, really.
Bus Stop #2, which is the Casitas stop, is the first one to get picked up going to the parks and the first one dropped off (provided the bus remains a park bus and doesn't switch to the DTD route). So, if getting a seat is very important to you, either pay for preferred (Casitas 1, 2, 3) or request Casitas 4 or 5. Ranchos is the next stop (labeled Bus Stop #3), followed by Cabanas (#4) and finally, El Centro (which is labeled at Stop #1). Since Cabanas and El Centro are the last 2 stops, the buses will be the most crowded when they get to those stops. Sometimes, yes, the bus is full and has to skip El Centro. (Note: buses going to DTD go in order from Stops 1-4.) I thnk if you use the stops in Casitas or Ranchos, you should definitely get a seat.
We have stayed in Cabanas twice - the first time we used El Centro (this was back in 2003) and the second time, we used Stop #4 (2007). We have been in Ranchos twice - first time we used Stop #3 (2008), second time we used #4 (2011). In all those stays at CSR, we did have to stand a couple of times going to the parks, but never had a full bus drive past us. I will say that on our last stay in 2011, after we got on at Stop #4, the buses were usually pretty full and the folks getting on at El Centro had to stand. I probably would not use El Centro again after that experience. A lot has to do with the time of year you visit, also. Three of our stays there have been in Sept, which is a slower time for WDW, so everything in general was less crowded. Our stay there last year was in May, and the resort and the parks were more crowded.
Again, I don't think you need to worry about the bus service, but I'd lean more towards Casitas or Ranchos than Cabanas if you'll be there at a busy time.
Hope this helps!