As someone who uses inks for customs I thought I'd put my two cents in. Really, it comes down to personal preference.
I personally like that inks go on smoother without the need of an extra step to thin the acrylic. The brand I use is speedball and FW acrylic ink, never actually tried india ink. The Fw is amazing and is currently my favorite because it behaves like an acrylic but is very smooth and easy to use. My method is out of the pot with brushes of varied thickness.
The best way to eliminate smudging when it comes to the ink is to have sealant you can spray on, like testors dullcoat. I wash the pony first, hit it with one or two coats of sealant, let that dry and then the ink has a surface to grab onto, instead of just running off the pony. I had to do this when painting a small G4 because while the head was porous enough to take the ink, the body is a different kind of plastic and it was just running off.
And, because Arkillian actually mentioned Guache just thought I'd share that I gave the stuff a try and for me, it didn't really work. It refused to grab the surface even after a base coat of sealant. Perhaps someone will have better luck with it than me. I was using a bargain brand of the stuff.
Good quality guache is also super expensive for the amount you get per tube so for me, it is not a preferable material to use.