Johto, because it feels much larger. (I haven't completed DP yet, so maybe I'll find Shinou better.) In Houen there are so many things that at first seem useless, like a cave that you need E-reader, and a lot of other things you have to connect your game to something to get to. And Kantou is too small. Johto has a lot of secret paths and caves that makes the region seem larger than it really is.
Shinou is supposed to be bigger, but then there this: the rooms may be larger, the roads wider, but how many rooms are there and how many roads? Maybe Shinou will turn out to be equal to Johto or even more. I'll have play through DP to see.
And the Pokemon in the regions. Then the best must be Kantou (FR/LG only) and Houen, because of the good place to EV train. I can't find many good EV training areas in Shinou. I haven't cared about Johto and EVs because you EVs are not so important in GSC.