Brony Galore, mom no hime can have whatever they want for their signature. The picture was made for them, and they like it, so it's their signature. There's nothing wrong with that.
You said it would take you two hours to make a vector. How much would that cost at, say, $7/hour (assuming you're ONLY being paid minimum wage?) $252 for all 18 characters. Of course it's going to cost a lot more than that, as they'll be professional graphic designers who are also going to be doing tests to make sure that they're printed color correct while being printed THOUSANDS at a time. And it's more than just the pony vector, it's the entire package, which will include the vector on the back, the text, and the phrase "pony wears the saddle" or whatever.
That's a lot to do. That's going to take longer than 2 hours for each of the 18 figures. And EACH ONE will have to be tested to make sure they are printed the correct colors, too. Picking colors is more than just picking what's pretty, it's making sure that whatever printer you're using can physically make that color.
Each printer has its own inks, which each have their own formulation. Just because printers use CMYK doesn't mean that HP's K is the same color as Kodak or Xerox's K. Each company uses its own pigments. Even different series are different colors.
I've worked on presses and mixing inks for years, and it's not easy. Making 18 packages is already a huge deal. G1 got away with this by having the same pictures on the package and only changing the name on the front and the story on the back, which is only changing WHAT the text is, not the size, color or location. But G4 changes a lot more, which takes a lot of work.
Don't even get me started on the die-cutting of the little front part of the G4 packaging.
So by color-swapping the vectors, they're saving themselves countless hours of testing and time, which saves Hasbro thousands of dollars.