The beaches in Samui are just as nice as the beaches in Phuket. The only real thing they lack is a bit of surf, since Samui is in the South China Sea and doesn't get swells like Phuket which is in the Indian Ocean.
On the other hand Samui is much less crowded than Phuket, and in off-season you often have the beach to yourself. That's a major plus for a lot of people.
Phuket: Much bigger and more developed, more services available, more expensive, beaches with waves. Easier to get to both by air and overland.
Samui: Quieter, less expensive, no surf, less major shopping centres etc. Harder to get to since only 2 airlines fly there and there is no causeway to the Island so you have to take a ferry if not going by air.