You get 1 at the beginning when you first start (during the tutorial).
You also get 1 from participating the Lucario event (now past).
You can get a maximum of 2 jewels from Streetpass (1 for your 1st and 1 for your 100th).
You then get 1 every Mega Pokemon you beat, along with their Megastone.
- Mega Audino
- Mega Ampharos
- Mega Altaria
- Mega Lopunny
- Mega Kangkaskhan
- Mega Sableye
- Mega Slowbro
- Mega Mawile
- Mega Gengar
- Mega Glalie
- Mega Mewtwo
15 Jewels in total. I'm not sure if you get another Jewel for Mega Lucario if you rank high enough.
I think this is correct; someone please correct me if I'm wrong.
List of Pokemon in Pokemon Shuffle