in flight (apart from the flight time) no difference. At a stage a year or so ago they were still flying A340's into Cape Town, and the J class seats weren't lie flat. Thankfully they stopped this (or at least, I haven't seen one for some time) and everything is now 777s.

Cape Town is a less busy airport, the duty free is pretty useless, priority boarding frequently isn't and the lounge that Emirates uses is crap (if you have a choice, use the upstairs lounge - don't let them take you through to the downstairs area). In the air, Cape Town is a way more pretty approach