Hi
I've used Intercape twice, once CT to JHB, and another from CT to East London. And I plan to take the Intercape to Namibia at the end of September. The Intercape is very good and very comfortable. Because it's a reliable bus line it can be full, so don't hope for an empty seat next to you. There are several stops along the way even if short, but they make sure you get back on. And I agree with ghalied, top deck is better (although bottom is ok as well). Booking with Intercape is also very simple and the call centre is very helpful; I've called several times and always had great help!
I've also used CIty to City once which was fine but they have 5 seats per row, instead of the usual 4, so it really felt very tight.
When getting off the bus at the rest stops make sure you take all your essential valuables. But that's just common sense of course.
Can't say much about the train. Would love to do it myself one day!
Enjoy your bus/train trips!