First, we could vote directly for (any) party in the European Parliament, so opinions not reaching the threshold in some countries still could be represented better. And it would make it less likely that people just vote their favorite local party.

In other areas:

For the ChatControl, there should be something so a regulation can not be proposed again and again and stopping just before voting it down.

There should be a way for making EU-wide referendums whose result is binding / obligatory for the EU (council and commission) and thus for member states, too. (This is probably hard if you want "better representation" of different sized countries and probably there would need a fairly high bar for passing.)

Make the European Citizens' Initiative easier / clearer, it could be a simpler, less formal, non binding option to an EU-wide referendum.

I completely agree with you.

Indirect democracy is just oligarchy with extra steps