Regardless of how easy it would be to store 3 million files in one directory on an ext3 filesystem, it would certainly be possible on an XFS filesystem.

XFS has been designed from the ground up for massive scalability, and has been in the mainline linux kernel since 2.4.25 or so.

XFS has dynamically allocated inodes, so running out inodes is never a problem.

I have personally used XFS as the root filesystem on my home computers for years, and never had a single problem with it.