Well, now that you guys brought EGM to the table...
There was this (apparently) spin-off called "EGM²" (yes, ²). In its November 1995 issue if I recall right (cover had Thanos and the main story was about Marvel Super Heroes) they had a walkthrough for a beta version of X3 - down to the boss names and weapons still being in Japanese and what have you.
The most obvious difference I could sight is that Bit and Byte's sprites are different from the final version. But I took a closer look at the article, and there are some other different sprites for some of the eight bosses, as well as some swapped backgrounds. Nothing nowhere as enticing as removed bosses, but a curiosity nonetheless. Here:
Catfish's and Buffalo's sprites are different from the final versions. If Sprites INC is any notice, Buffalo doesn't even have that dash pose in the final version.
Tiger's sprite also seems a little different, and his background and the sub-boss' were swapped in the final version.
And the most glaring differences, Bit and Byte: