Well I prefer writing music with my acoustic, but that's just because that's the genre I write the music for.

It's just preference, really(I think).
Today I feel electric grey
I hope tomorrow, neon black
I usually tab out the chords on my acoustic, then switch to electric to add riffs and solos and such.
But like Ganoosh said, it's really a matter of opinion.
Writing songs on an acoustic is great. Just about any song written on an acoustic can usually be adapted very easily to an electric, but not all songs on an electric can be adapted to an acoustic.

Here are some guidelines that I like to really follow very closely:

If the song has positive emotions to it or evoked from it (such as love, tenderness, happiness, faithfulness, excitement, joy)

If the song has negative emotions to it or evoked from it (such as pain, sorrow, sadness, anger, loss, hate)

Now there are exceptions to these, and each song its self will determine the exception. Some songs that you may think would be acoustic only may fit better with an electric, and some songs you may think would fit better with an electric actually would fit better with an acoustic. Then there are some songs that actually have acoustic and electric parts in the same song. And finally, there are the songs that will work great either on an acoustic or an electric.

It really is a matter of your own personal taste, and what you want your music played with. But keep in mind, if you want others to enjoy your songs, you must use the instrument (or instruments) that will get your song's message across most effectively and most pleasantly to your listener's ear.

So just really think about what you are writing, why you are writing it, and who are you wanting to hear it. Answer all of those questions to yourself, and I am sure you will come up with either the acoustic or the electric as the best choice for the particular song you are working on.