In the 2012 Toaplan STG Chronicle interview (released as a bundle alongside the Toaplan STG Chronicle music collection), the game's composer Tatsuya Uemura confirmed that Zero Wing was originally just a test project for new hires and that it wasn't meant to be released commercially. Mr. Uemura stated:

"This title was created as a training project for our new hires. At that time we didn’t have any plans to release it commercially. But the decision to release it commercially made it a much more practical learning experience for the new developers, I think. On the other hand, the stage design and characters were rather cobbled together, so the world of the game was kind of a mess."
Contributed by ZpaceJ0ck0
A line of dialogue was removed from the intro sequence in the English version. Said line translates as "thank you for you cooperation".
Contributed by ZpaceJ0ck0
The game has 32 additional endings exclusive to the Japanese version. No official explanation has been given for the removal of these extra endings, but considering that they rely heavily on unusual speech patterns and pop culture references from the 60's and 70's, as well as the poor quality of the opening's translation (the source of the famous "all your base are belong to us" Internet meme), it's fair to assume that the localization team didn't translate the endings because it was possibly beyond their ability.
Contributed by ZpaceJ0ck0