The UNO R3 can easily have the processor replaced if you damage it. With the SMD you throw the whole thing away and get a new one.
Another nice thing about the R3 having a socketed, and therefore replacable, main IC is that you can use R3 for initial sketch development, testing, and chip programing; then use the program chip on a custom PCB. This is especially nice for projects where USB, or even FTDI headers, won't be used in the final project. Therefore adding external communication just to program the chip would be inconvinient and require more space, time, and (albeit minor increase in) cost for something that's only going to be used once. Similarly you can also create a "library" of pre-programed chips for back-up or to temporarly change the function of the board without having to connect it to a computer and compile a sketch.
That stated, I have and use both R3 and SMD Uno boards. If you want to dedicate a stock Uno board to a particular device, the R3 has no advantage over the SMD. It's all about using the proper tool for the job.