This is such an odd conversation. Vectors are tricky enough that usually people who can actually use Illustrator with enough skill to prefer it know enough about computer graphics to not have these sorts of questions. Illustrator graphics are always on transparent backgrounds, you have to purposefully add a background in if you want one, so there's no worries there. The difficulty I've always had in doing things exclusively in Illustrator is also its strength; vectors can be any size. This means that the scale is rather fluid, which makes it not as well suited for something like RPG Maker graphics, since pixel precision is needed at some point in the creation process. Forcing Illustrator to work for "computer only results" instead of print ones has always been a hassle every time I've attempted it, especially with the way the canvas works. I get where Celianna's coming from, especially since Photoshop has vector tools. Even importing things into Photoshop for the finish work is a bit strange, because things never transfer over quite as cleanly or the size you expect. I only have experience with it because I learned both programs back before Photoshop's vector tools were of any real use.
If, like I suspect, you're not an illustrator expert and are just looking for very clean lines, then you should just use whatever art program you're most comfortable with and not worry so much about the line work. All you really need to do is work at double the intended size and scale down, that will solve most if not all problems with unsteady lines.
