Here we go again... someone asking for the general design answer. If you're being serious about the question - which I think you are, or otherwise, you wouldn't have asked - then read through this post attentively. If you're the generic advice-resistant guy who looks for the golden answer solving all problems for all projects coming up, than take either solution - your game will most likely suck anyway.
So, it's not as easy as saying "Don't use Comic Sans wen designing any media"... there's lots of possible ways your (and everyone else's) game is set up, and with no information given, this is impossible to judge. However, there's usually some cases you can tell that won't work likely. Let's have some...
1) A skating game wouldn't work with small areas, as you have to be able to move quite a bit.
2) A Sokoban-styled game would be more annoying than interesting with giant, unnavigateable maps.
As for the points you've given... small maps don't have to be annoying, they have to be utilized correctly. Take a look at games like Zelda 3 (LttP) and 4 (LA), which only consist of screen-sized maps, yet scroll in a way that makes you think of them as larger areas, which actually adds to the gameplay, as the action is kept to the current screen - the player never looses the view over what's happening at the current area.
The other thing are empty maps... while you clearly talk about a RPG-Maker-typical problem, there actually are a few games out there who were basically empty, yet interesting. Take most of the early vertical scrollers - noone complaned about emptiness back then, because it was the gameplay that counted (sad that it seems to be different nowadays). And of course, there's newer games like Shadow of the Colossus, which had that giant worldmap that had NOTHING in it, yet was cool to travel through, because that was your objective, and the world was designed beautifully (being my opinion, I know there's different ones out there).
Bottom line: Analyze your game, and try to figure out what mapping style suits it best. Thinking of what the player might feel like when he plays it is a very good start (considering how some "professional" game designers don't even think of it...), but annoyingness vs boredom won't get you a good solution anyway, so you have to figure out a way to eliminate both cases.
Good luck!