number 1 is pretty much the same thing actually. number 2 is different because it indicates the quantity of good points while the other sentence does not. "You have made very good points." means you made 2 or more good points. "You have made a lot of good points." suggests you made many points.. so 2 is not enough. "a lot" imo would be atleast 3 or something.

Point = an idea, opinion or piece of information that is said or written "You have made very good points." = said to show that what someone has just said is true or important

I think it is the mean that you have say the key word...I hope it can help you!!