I voted other.
I firmly believe a game should take up all the window, if you're looking at a single screen (as all PC gamers do). A dual screen is fine for the 4th Gen games, because the DS has two screens (no, it does, I've checked), but when you're playing on a PC you only have the one big screen. Turning half the game window into a menu just begs the question: "why not make the game screen bigger?". I have no problem with pressing a button to open a menu, since that's how practically every game ever works.
Having half the game window being taken up by a menu just distracts from the game itself. It feels like the menu is just as important as the actual game, which it clearly isn't (so why give the two 50% of the screen?). And it is always "half the game window" - people don't seem to have imagined that the lower part can very easily be smaller than the upper part.
A side bar is better, but if you must have one, make it as unobtrusive as possible. We're here to play the game, not look at the menu. It's better because it's different and would be potentially smaller. Not that a lower screen can't be a small strip either, but no one seems to have realised this. In fact, rather than a side bar, try using a lower bar that doubles as a text box during conversations. You get more game screen to play with, since messages are displayed below it, and because it's a bar you can simply make some screens (Summary/Dex?) a bit taller, rather than keeping a strict line to say "this is one screen, this is the other".
Having a menu visible at all times breaks the immersion, too. It's harder to feel like you're the player wandering around the world when you can always see the Save and Options buttons right there. D/P/Pl was better than HG/SS when it came to having an idle lower screen, because it showed the Pokétch, which is still part of the game. A menu, not so much.
An interesting (and disappointing) feature of all fangames that have dual screens is that they all seem to use it to display a menu. As I said, displaying the Pokétch is a better idea than a menu, because it's still a part of the game. But no, people think newer is better, which is why everyone wants to mimic HG/SS. I actually think better is better, but that's just me.
And then we get to the idea of a touch screen. I don't know how other people have their computers set up, but I have my keyboard here and my mouse here. I don't want to have to switch between the two at all during a game, and if I do just let it be for minigames. Don't make me have to keep moving from the keyboard to mouse every time I want to check whether my Linoone has found anything after a battle. That's just bad controls.
The DS is excused this because you can use your thumb, and the touch screen is right next to the controls anyway (and it's a major and popular product of a huge gaming company, which means it can pretty much do whatever it wants and people will love it). Fangames don't have the leeway to be half-arsed - for fangames, a small flaw is a flaw nonetheless, and people will pick up on it. A better game is not the same as a more technically advanced game, so don't put in features just because you can - put them it because they improve the game.
The only thing worse than someone deciding to do a dual screen and touch screen "because that's what the real games have" is someone doing that and then keeping the exact same design as the official games. I mean, if you're able to implement something as complex as that, you could at least try moving the icons around. Aside from a redesign being trivial for someone of your skill, it'd be new, fresh, original and other synonyms for "not a mindless copy".
That's my rant over. I think there were some good ideas in there, and anyone is free to use them.