Everything the EU does can be done without these hacks (one alternative would be to negotiate acceptance of the directive as individual treaties), but the governing structure streamlines what would otherwise cause a whole lot more bureaucratic hassle by having created a legislative process which isn't really a legislative process, except that the member states have committed to taking the output (the Directives) and implementing them into law. This ensures that no legal delegation of sovereignty needs to be done, because national parliaments can choose to say no. There would be consequences, but they have the right to.
It also, despite the many flaws in how it is done, delegates some of this decision-making authority to the EU Parliament, something which is only possible because they're involved in deciding on Directives, not laws, because there is no legal basis for them to legislate. Even so, this involvement is limited because there is also no legal basis for Parliament to exercise the executive powers of the member states that is used by to actually bind the member states under the relevant treaties.
I don't think anyone (other than lawyers making money advising on it, perhaps) actually likes the current system. But it sort-of works, and the poblem with trying to reform it is that people dislike it for diametrically opposing reasons: Some wants a federation, some wants powers pulled back. So it's one of those compromise that makes everyone equally miserable.
We already have experience with this, in that the ECJ is already the highest court for matters of European Union legal matters, such as the interpretation of directives, and national courts in EU member states will often need to interpret cases in light of EU law.