A number of major changes were made in porting the game to the 3DO. These include:

Difficulty select was removed; the game can only be played at one difficulty, which roughly corresponds to "Veteran" in the PC version.
All stages set on planetary surfaces are cut, and replaced with Full Motion Video cutscenes. Staple mission audio clips (e.g. "Attack my target") are used for the dialogue in these scenes.
Manual takeoffs are similarly replaced by FMVs. The player starts each mission in open space.
The left VDU cannot be made invisible.
Several enemy types were removed, including all land-based enemies.
A new enemy was added, the gun platform. This enemy is stationary.
The ejection animation was cut, as was the option to retry the mission after ejecting.
The player must select a ship as a target in order to communicate with it.
The bug which prevents the player from accessing the cutscene explaining Hobbes betrayal in the PC version is absent.
There is a new bug in the first Hyperion mission. Unless all enemies in the mission are destroyed, this mission will register as failed, regardless of whether or not the player successfully used the bomb prototype.
Only two of the three possible endings of the PC version are accessible. This is because the removal of the planetary sequence makes it impossible to fail the mission in which the Temblor Bomb is planted.
The scripted deaths of the pilots in the Temblor Bomb mission were cut. Thus, it is possible to complete the mission with all four wingmen remaining.
The cloaking device works on Hobbes and Thrakhath, and thus the Temblor Bomb mission may be completed without fighting either of them.
The PlayStation version is much more similar to the PC version, though like the 3DO version it does not carry the bug which blocks off the Hobbes cutscene. Also, unlike either the PC or 3DO versions, it includes considerable load times when navigating the Victory.