As with any major building project, a personal observatory demands attention to a myriad of details, some obvious, some not. As one who has "been there," let me highlight a few potential problems that you might not see on your blueprints.
Location, location, location. Most amateur astronomers don't have a lot of choice about where they build their observatories. I am lucky enough to own two; one is at a distant dark-sky location, and the other sits in my front yard in Tucson, Arizona. Although the remote observatory houses a larger telescope under a better sky, I love my home observatory because I can walk out of the house after dinner and be observing in five minutes. If convenience is your prime motivation for building an observatory in the first place, it makes little sense to choose a location that takes an hour to reach by car.
Material matters. If you enjoy high-power views of the planets and double stars, beware of building your observatory with concrete blocks or bricks. These soak up heat all day and then proceed to radiate it away all night. The result is poor seeing at the telescope. Similarly, asphalt walkways and parking lots next to the observatory spell trouble. A wooden structure situated on a grassy lawn is probably the best combination for a home observatory.
Surprise costs. Observatory projects are similar to defense contracts in that they share a penchant for cost overruns. No matter how carefully you think you have worked out your budget, double or even triple it to arrive at a "realistic" estimate. There is a plethora of surprise costs associated with building an observatory: taxes, fencing, building permits, electrical supplies, and so on. It's better to overestimate and have money left over.
The twilight zone. It is wise to acquaint yourself with local zoning regulations sooner rather than later. In some municipalities or neighborhoods an observatory might not even be allowed! Be certain to obtain the appropriate building permits; otherwise you can look forward to an unpleasant encounter with local zoning authorities. In extreme situations, you may be fined and forced to dismantle your observatory.
More power to you. You can never have enough electrical outlets. In the planning stages, allow for as many outlets as possible for your telescope and other equipment. Don't forget to include a couple on the outside too. These are especially handy for the inevitable odd jobs and site upkeep. Be sure to ground your observatory. Make use of a high-quality surge protector, especially if your telescope setup includes a computer.
Getting protection. Sadly, in this day and age, it is important to protect your observatory from unwanted attention — particularly if it is located in an out-of-the-way spot. A good fence in conjunction with strong locks and a suitable insurance policy should afford some peace of mind. Vandalism and theft are always possible no matter what precautions you take, but it would be self-defeating to worry so much that the observatory remains forever unbuilt.
Vermin visitations. Animals love observatories but not for the same reasons you do. Wasps build nests inside; birds build them outside in the eaves. Rats and squirrels like to chew on wires and insulation while ants always seem to find whatever food you might have stashed away for a late-night snack. To avoid surprises it's a good idea to inspect your observatory regularly for new tenants, especially in dark recesses where rattlesnakes and scorpions like to take refuge. Some animals are worth having around, though. I once foolishly ejected a gopher snake from my observatory, only to realize later that it kept the rodent population under control.
Plan for the future. Today's telescope might be a compact 8-inch Schmidt-Cassegrain, but will it remain your telescope of choice five years from now? Will your observatory accommodate that 10-inch equatorially mounted
Newtonian that you decide you absolutely must have for your CCD asteroid-search program? It's never a bad idea to build in a little elbow room for guests and those extra pieces of equipment that inevitably find their way into any well-used observatory.