In 你说的是什么？, what is the purpose of 的?
A reasonable translation of "你说的" is: "That which you spoke".
的 turns 你说 (a verbal phrase) into 你说的 (a noun).

你说是什么 doesn't make any sense grammatically - it means "You said is what?" You can say, "你说什么" - which is literally, "You said what?" or in proper English, "What did you say?"

你说的是什么, however, means "That which you said is what?" or properly, "What is that which you said?"