First thing you want to do is pick out the engine. I tried to work with it once and I got a bit stumped.
There are some naturally English versions of the game, but I'm pretty sure that they're harder to get and have less in terms of resources available.
Pros of 2000
+The engine has a sort of... what is it, Dragon Quest? That sort of battle set up. That means you don't actually SEE the player characters in battle, so you only need a spriteset for wandering around and cutscenes and the like.
+The engine is generally simpler to use, I've found.
Cons of 2000
-The engine itself was translated from Japanese to Russian to English. Naturally, some things are NOT going to look nice. You'll even find with the included stuff is a demo game that has you choose Russian or English (and the English is just awful)
-Because it's a simpler engine, you'll have less customizability.
Pros of 2003
+The translation is MUCH BETTER. Like for serious, the difference is AMAZING.
+Pretty sure you can add many more characters.
+The engine is more fleshed out, so it's got more to tweak and the like.
Cons of 2003
-The engine is more complicated and has a lot more you'll be working with.
-The battle system is Final Fantasy styled, so along with walking and stuff like that, you'll need a battleset. These can by really intricate sprites or even just rehashes of the walking sprites (ala FF6)
Both are REALLY good choices, and I'm more familiar with the two of them than I am with the latest stuff. What I'd suggest in terms of sprites is looking up the charas generator and getting just a blank body, then drawing the clothes and such onto the characters. That way you don't try to draw a character from scratch and end up with something that doesn't fit into the frames.