The problem is that those laws are not modifiable because you need the unanimity of all the countries in the EU. Which is extremely difficult because, again, all the 28 countries have different interests in all areas of the treaty. It's basically stuck.
As far as you saying that every member state can have its own set of rules, no. We had this issue multiple times and found ourselves having to pay insane amount of penalties because we were not, for example, accepting to grow GMO in France. If the EU says "You guys should do this and that in that matter", we can't have a rule that goes against that. That is the real problem, I think that the people of each individual country do not decide anymore, and the people in charge have no power, since they cannot take their own decisions.