The game features a completely rewritten game engine, new graphics and sound as well as digital music (a la MOD files), along with a new style of game board and an additional "special weapon" for each figure. It also adds multiplayer game (modem as well as hot seat).
Archon Ultra is obviously based largely on code from Star Control 2 as it also suffers from some of the same bugs (sound hanging under Windows as well as color corruption with newer VGA cards). Unfortunately, the bugfixes that apply to Star Control 2 do not apply to Archon Ultra.
They also didn't test their sound library, DSMI, with Gravis Ultrasound cards, which require different handling. On a machine with a GUS, the sound is very slow during idle time.