Rika was initially meant to be Nei herself from Phantasy Star II as was said by Tohoru Yoshida in an interview; conflict within the staff compelled him to make subtle alterations to keep Rika in.
The game was originally supposed to get a full remake that would have been at least on par with the PS2 remakes of Phantasy Star I and Phantasy Star II, but it was cancelled when they decided to retool the PS2 Sega Ages series as straight ports.To twist the knife deeper, this also resulted in the US releases of the other remakes being cancelled, as they were planned to be released in a compilation set with this one.
An early concept for the game would have seen Alis(a) returning to the series, and this is what Phantasy Star Gaiden was setting up for.
Also, early concept art and magazine articles stated the game was being worked on as a title for the Sega-CD with a tentative working name of "The Return of Alis". Just imagine, a Phantasy Star game with redbook audio and enhanced graphics that very likely could have saved the console had it been made.
Taking the above into account, with a cameo of Luts, the wreckage of one of the ships from III, Nei, and a return by the franchise's main heroine, it would have brought back all the iconic elements of each game for an even greater finale than what we got. As it is, these elements are only vaguely implied by the game itself.