I don't really know much about pixelart...
most people will probably be running game at high resolutions anyway from at least 1024x768 & upwards so I wouldn't worry too much about degradation of graphic quality when scaling down.
if you are planning on releasing the game for iOS (iPad) then I would recommend keeping the game around 1024x768 so that the game doesn't require too much ram/vram to function & will still look fairly nice, even on larger resolutions.
by default the game will be set to full screen mode & resolution auto but you can also force the game to display at whatever resolution you want with bounding box/borders around the edge. this can be done inside of the config.ini file which gets created when you compile your game into a playable executable (.exe) file. there is a slight issue with this though as it does not center the game to the screen & instead is usually aligned to top left of the screen. I keep meaning to ask about/mention this to the devs - bad memory!
you can technically force the scale (in %) for active animations via the use of Lua Script but it has to done for each animation, each time it is played.
Besides Pixelart is never going to look that crisp on high resolutions anyway - it's pixelart.