Phantasy Star IV, like the original Phantasy Star, was going to have 1st person dungeons, and battles. This was later dropped, in favor of the more common, 3rd person perspective. Much to the dismay of many 1st person advocates;)
Many items did not make the final cut in PSIV: the Blood Axe, a weapon for Gryz; a map similar to that of PSIII's "monitor"; a technique that when used was to fully restore your party, like healing at an inn (called "Resta" if memory serves correctly), as well as the return of the Skure Spaceport and the Nei Dungeons from PSII.
These appeared in a beta version of the game and can be accessed via a ROM. But the Skure and Nei Dungeons cannot be entered.
In the English Phantasy Star IV manual, it is written that there are 15 combination attacks, when there are actually only 14.
In Phantasy Star IV, there are cameos from previous Phantasy Star characters. Alis, and Myau appear and speak to you, while the rest of the cast of Phantasy Star and Phantasy Star II also make a non-verbal appearance.
Almost all the names of your party members in the game were changed in the English translation. Some changes were probably necessary, since there was a four-letter limit for names written in Latin letters, while the Japanese could write longer names with their kana (syllabic letters). Other changes are seemingly without any reason.
Here are the names in Japanese and English versions, respectively:
Japanese: Rudy, Fal, Lyla, Pyke, Thray, Forren, Freyna, Shess.
English: Chaz, Rika, Alys, Gryz, Rune, Wren, Demi, Kyra.
There are books on the bookshelf in Saya's house that reference Sonic the Hedgehog, Ecco the Dolphin and Golden Axe.
Phantasy Star IV was at one point going to be a Sega CD title, but about midway through development, Sega promptly cancelled the Sega CD version and stuffed it onto the Sega Genesis instead. Why did they do this? Blame it on lousy sales figures for the Sega CD ( and blame the lousy sales figures on crappy FMV games ^_^).