I can't really say. I started with Photoshop, which of course has a learning curve of its own, and moving on to SAI I find it lets me do certain drawing and coloring tasks better (or, at least, I feel I'm able to do certain things more easily/intuitively) than Photoshop. Just having that 'Marker' function was, to me, pretty neat. And I'm still just picking up the basics with SAI.
The only other art program I've really used at all is Manga Studio EX, which is pretty cool, too, though more expensive and really oriented toward making comics (obviously). But Photoshop is what I learned in art school, Manga Studio I got on sale (and saw Doug Ten Napel doing a demo with it), and SAI I learned about from watching people make anime-style art on YouTube. If there's something out there that works better than these, I'm unaware of it.
Oops, forgot to add: I've been omitting the tip of her nose in an attempt to mimic the look of the sprites in the game. To be honest, I'm not entirely sure I'm happy with that aspect or not; I'm still trying to get a feel for the shoujo style, but I've noticed that not all shoujo artists (including my favorite Katawa Shoujo artist, ) do that in all of their work, either. I appreciate the critique!
What I imagined Hanako thinking when I was drawing them were:
) = "'I'm Shizune and it's okay if *I* skip class because I'm on the Student Council, which is oh-so important. Watch out or I'll give you the evil eye!' Bleah!"
:3 = "'The Land of the Sword-Storm' just got translated into Japanese! Looks like *somebody's* got plans for the weekend!" ('Land of the Sword-Storm' being the Japanese title of George R.R. Martin's 'Storm of Swords'.)