I have been testing the free version and there are a few things which i find annoying:

1. Importing large SQL files into DB is slow, SequelPro seems to be much faster;

2. No option to add/delete connection when you choose "Show connections";

3. Maybe it is a free limitation but almost every time i want to open a table it wants to create a new tab;

4. It doesn't want to reconnect to the server (even when cmd +r) if it lost connection - must close and open server again;

5. I have noticed that 2 different databases which are exact copies (structurally) have different column order so doing simple cmd + c in one DB and then cmd + v will mess up the data as the column order is different.