Assistants is an agent framework. Your instruction is similar to a system prompt, but is just one part of the message that includes other messaging and internal functions that are out of your control.
Assistants allows the AI, and the AI is encouraged to, make multiple calls persistently in calling for retrieval of parts of uploaded documents via internal functions, writing python code and emitting it by function to a sandbox that can run the code, and then finally emitting functions back to you in similar fashion to chat completions.
It also has a record of user input and AI answers that make up a conversation, only allowing you to place a user question, run the thread, wait for an answer to be created, check the status, and then download the finished answer. Or you find that the AI has been waiting for you to run a tool function for it.
The AI is loaded with the maximum amount of conversation and the maximum amount of documents that will fit in the model. There is no token usage statistic in the API return to show how much you will be billed.
So, the advantage is that some things that people were doing themselves can be done - but with coding made more complex just to interact with the API. And the disadvantages are great, no control.
Here’s a post where I laid out the inputs to tools (as a function API replacement only for preview models) and what you receive back, and then what you fulfill. In programming, much of what you see would not be as illustrated.