You shouldn't need a flatpak solution, installation isn't complex. The only dependency for installation is a Java installation, openjdk-{version}-jdk-headless on Linux normally works fine and should be available in your repos.

Once you've got Java installed, downloading an installer for I2P+ and then running java -jar ./i2pinstall.exe or whatever the name of the download is will launch the graphical installer. Running ~/i2p/i2prouter start post-installation (assuming you installed to ~/i2p/) should start the router and launch the console in your browser. Additional instructions available on skank.i2p.