There's no denying that the game was originally intended for 320x240, and all the graphic and level design were done with that in mind. Many of the official levels look a lot more barren at larger resolutions because never much attention was given to wall areas significantly distant from the main path, and you can see secrets and stuff you probably shouldn't be able to. The higher resolution also has something to do with JJ2's difficulty being lower than JJ1's, whether you think that's a good thing or not. But as screen resolutions grow ever larger, 320x240 grows less palatable, since it's hard to see anything in windowed mode and the game's incredibly pixelated in full screen.

Ultimately, yes, certain tilesets were designed for 320x240 and 320x240 only, though nearly all the official levels (discounting, for instance, Haunted House) make good use of the Limit Visible Region checkbox, whose sole purpose is to accommodate multiple resolutions. But people like being able to see more, and trying to counteract that in any serious way, especially multiplayer when you have to be able to see your opponents, isn't really a fruitful pursuit. Just take it as a challenge.