I can not tell you what -you-shall do, but I can tell you what -I- do!
I always draw the coastline first in photoshop. If I want an old-looking map I draw a simple line with an ordinary small brush and try to variate the coastline. If I want a more rough, realistic looking coastline, I usually draw the continents as I just described, but then I work the coastline once more with the eraser and a scatter-brush. Tweaking the settings to get that random jagged coast. Make sure you fill the "land" first before working on the coastline this way.
I wouldn't worry much about climate, astronony and geology. I'd say - let those features adapt to the map instead of the reverse. If you decide to put a mountainrange "right there", then there is probably two plates just under.