1024x768 is too big for a windowed game; I use 2048x768 dualscreen and it's annoying to have a window bigger than one monitor, and by the stats a lot of people still use it single screen anyway.
The screen is also redrawn fully every tick so there's the issue of rendering speed if you have a lot of heavy rendering going on - smaller windows will generally render faster.
Then there's the issue of VRAM usage - textures are always put on power-of-two sized surfaces in VRAM, and the runtime has to create several textures the size of the window sometimes for purposes like effects rendering. If your window is bigger than 1024x768, these runtime textures now have to be put on 2048x2048 sized surfaces, which could potentially use a lot more VRAM.
You can use the 'change display resolution' though to set whatever resolution you like at runtime; this would be handy for users to pick what they want. It might be wise to start up the first run with a small window, allow the user to pick their display resolution and fullscreen setting, then use the system actions to set them when the game begins.