I can't think of any real negatives on II, you sure you are not thinking of III? Civ2, cannot remember much about it now. It was my favorite, but it was just too easy to win at any level. Too many exploits and I hate the kill one, kill the stack. I also hated caravans.
Moo1 is my favorite game, but II is very very close and I sometimes switch them as my favorite. Being able to upgrade ships adds a lot. II also has MP, I does not.