The window size parameter won't affect quality unless you have the low quality option setted, so it is more a convenience and aspect ratio base rather than a huge decision (assets will define the quality by themselves, so you should worry about them). 800x600 is fine for html5 portals too since they will use the window size as the setted window size on said portal (which bothers me when your game can scale up and down)
And even with a chosen aspect ratio, it is best to ensure your game adapts to other display (which is not as difficult as some think, it all depends on the game, some will be sorted with a simple scale outer + unbounded scrolling + anchor behavior on hud and menus elements, other will have to be rzplaced with the event sheet.), it is just something you have to prepare for beforehand (I remember a project where someone hard coded every position with direct numbers like 800 rather than relative positions of the borders, in retrospect it was a real mess to work with this code anyway, if you want to target multiple screen size, try to see when something has to be placed relative to a corner or a border of the screen or not, that will be at least the first step)