I think that mainly has to do with how they're ripped more than how they actually are in the game...since the 3DS is kinda a funky thing to just hack into in general. Most of those sprites in that compilation I linked you to are "cleared" meaning that you don't have, like...50 different tiny variations of one color, and some aren't. Your best bet would be to clear / recolor them by hand. :>

As for Bulbasaur, your best bet would be to get rid of the stray pixel next to its farthest eye and just make it a straight shot. Adding a little corner to the top-left of its head will also help, too, as to make it at least seem like the ear is there. I'd also put fewer striations on its bulb, since, when you go smaller, sometimes you have to sacrifice detail to get the bigger picture to turn out better. Which is why it's more ideal if you start out doing something of a more...ideal size, maybe, but hey, that's to your discretion. Start off with what you will! :P

Ivy also turned out pretty good but the leaves off behind its head are non-existant. By the way, just out of curiosity: how much do you shrink these before you edit them, anyway? Just wondering because this is just adorable and I'd like to try it out sometime. >w< And by reducing the size to half, it's just...a bit too small.

As for Venusaur, when you shrink the sprite sometimes you get mashed up details that are just...too far gone, so you usually are best off erasing and adding your own in there rather than worry about fixing them. This is also easier to describe with an example, if you don't mind. :>

You can probably see that the shape of the flower is...completely different. This is because I just erased all the little details in the flower and just reworked said details and the shape, especially. ^^

And heck, why not? The XY icons are great. 8D And yeah, when I was using Paint I'd just use Paint.NET for transparency purposes. ^^