I don't. Really. I understand your feeling on this, but I gave up long ago on including enemies in any of my maps because my need for perfection compels me to put them in their exact starting position (down to the pixel) which is often hard to determine because they usually start moving a bit before they appear on the screen. Imagine how long it would take if I waste 15 minutes for every enemy in an entire game!
It's hard enough when I include moving platforms and dynamic objects for the same reasons; their only advantage is that they usually move in a set pattern so it's easier to determine a standard for where to put them on a map (like the highest position for a vertical moving platform).
Also, I want my maps to look *good*, even if it means leaving normal enemies out if they clutter the map too much. And in some maps like for Battletoads (NES) which I'll resume working on someday, there are just to many enemies. While the screen stands still, you'll be attack by 3 or 4 enemies appearing on the borders of the screen, then while it scrolls slowly, more enemies appear on the border, but when placed on a map, you end up with 4 or 5 enemies right next to one another, which looks stupid and ends up hiding the stage itself.
And in the end, it comes down to not wanting to bother with the trouble really. I once wanted to include all the enemies all the time, but it took me twice or trice as long to finish some maps, and considering that some of them took me several weeks already without the enemies, you'll understand that it's a compromise I've made with myself so that I would accomplish more (and since I already start a lot of stuff and never finish 90% of them, you can see why any tiny amount helps).
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Current projects: Ristar-The Shooting Star (Gen), Sonic The Hedgehog (Gen), Sonic CD (Sega CD), Mega Man Zero (GBA), Battletoads (NES), Bucky O'Hare (NES)