How can I make controller ports round for my "Lego Gamecube"
Perhaps something like this using 1x4 arches could work?

This does work out to being 2 modules too wide for 1:1 scale with a GameCube, but the trade-off in accuracy may be worth it to you to get the round ports. It appears to be only 1 module wider than your current design.
Here's more detail of the build steps:
Step 1

Step 2

Step 3

Step 4

Step 5

Final Build