Both kits have the same functionality: A cycle-accurate emulation of the original Altair, USB port for connection to a terminal emulator on a laptop or desktop, a DE9 serial port, emulation of the Processor Technology Music System, a micro SD card with floppy and hard disk images, and a VT100 emulator with VGA and USB keyboard connectors.
The primary difference is the size. While the Altair-Duino Pro is an extremely accurate reproduction of the original Altair, it takes up a lot of space (17" x 7" x 18"). The Altair-Duino Experimenter is smaller and can easily fit on a shelf to display in your home or office (with a size of 15" x 6" x 2.5").
The Altair-Duino Experimenter is also much less costly to ship, which can be especially important if ordering from outside the USA.