To highlight a few things:
1. The 488 (essentially the 458 design) is about 15 years old now... So the Emira has a 13-14 year advantage over the 488. Remember the Aventador is about 15 years on the Diablo, which is in turn 20 years on the one and only Countach. The EMIRA is able to take advantage of some of the design ideas from the 488, while the Ferrari can't do vice versa. Also the design tools and 3D simulators and aerodynamic tools are way way ahead of those from 15 years ago.
2. The Emira is a bit shorter and the lines tend to be a bit tighter, and slightly more muscular if you look at the detailed quality of the curves. Imagine 400m Olympic runners vs 100m runners.
3. I do agree the Emira has a few things nicer than the 488 but to me, it's like compare a 22 year old girl against a 36 year old girl.