Actually, shorting the handshake/control lines doesn't make the connection any better. It just cheats the PC into thinking the other side has accepted the handshake, so if I by mistake turn hardware flow control on in PC, the connection will still work - it's not about adding a feature, it's about removing an annoyance. (MCU never hears the PC's handshake signals, they just return through the cable back to PC on other lines as fake "OK" replies.)
I intend never to use them, but accidents happen and I prefer to make connections between 5 pins than seek for hours why ISP doesn't work, and it doesn;t just because hardware flow control was turned on...