Absolutely! But there is a good reason for that. I first got into building my own wheels out of necessity. At the time I was commuting 40 miles round trip every day, 5 days a week and doing longer rides on the weekend for fun. During this time I did not own a car so I put a ton of miles on my bike. I kept breaking spoke after spoke after spoke and I finally got fed up and built myself a set of Open Pro's laced to Chris King hubs and never had a wheel problem again, even doing some light touring on those wheels in the middle of my long commute. This was the beginning of my love affair with custom wheels.
Not all wheels are created equal, even when from the outside things look almost identical. Take the wheels above, both have carbon rims, Sapim CX Ray spokes, 24 hole count, built to the same standards, surely they are the same right!?!? Not at all, while both wheels could be used in similar conditions there are some small but key differences that will really make the difference when pushed. The wheel on the left will be used by Kurt Searvogel to get him to the end of his attempt at the highest annual mileage record and is shooting for 80k miles in 365 days averaging just over 200 miles EACH day, he is currently at around 50k miles for the year... The wheel on the right will be raced by Fernando Riveros Paez and is likely going to see the podium in a number of pro level cyclocross races. The set ridden by Kurt has a few changes that should significantly increase its life over something like the wheel ridden by Fernando. Things like a higher quality hub, brass nipples, slightly heavier rim that can take higher spoke tensions are all small changes that should have a big impact on durability. On the other side, the wheel ridden by Fernando has a cheaper hub because being race wheels they will not see many miles, it also uses aluminum nipples and a lighter rim to help acceleration on the race course. While this wheel is sufficiently durable for its intended use I would not have much faith in it if I expected it to see 10k miles or more which the wheel for Kurt should easily do. These are just two examples that stood out because I happened to build them in the same day and it hit me how drastically different the operating environments will be despite seemingly similar design.
Most of us do not fit in the middle of the cycling bell curve and we all place different demands and expectations on our equipment, even during the same style of riding. A 130lb climber will place different demands on their equipment than a 180lb sprinter even if they are both in the same exact race at the same time. The climber could benefit from a 20 spoke super light wheel when under that 180lb sprinter would feel like a noodle that flexes so bad it rubs the brakes when they stand to pedal. Even if you don't race you can still benefit from fine tuning your wheels to your riding style. Someone who rides 12k miles in a year might be willing to make some slight performance compromises to maximize comfort and durability and the rider who loves fast club rides but sees much more modest miles might sacrifice comfort for an aero edge.
If you do big loaded tours, well...no one really has good "off the shelf" options for you...
The same can be applied through all areas of cycling, commuting, touring, mountain biking, etc. We all place different demands on our equipment and with wheels being one of the biggest changes you can make to how your bike feels, it seems like a shame to just go with a cookie cutter wheel aiming for the "average" cyclist.
So how does one customize ride characteristics of a wheel?
Comfort is a big thing that can be changed through selecting the best components for your riding style. Box section rims tend to have a more compliant ride than deep aero rims. Shallower rims also are less influenced by cross winds than a deeper rim making it easier to control the bike in windy areas. Rims come in all sorts of different depths, everything from your traditional box section rim like the Open Pro all the way to 80mm or deeper rims, usually in about 20mm increments. The trick is finding that balance between comfort and aero that fits your riding style best.
From a performance standpoint, you obviously factor in aerodynamics with things like rim profile and depth but also throw in things like spoke count, spoke type, hub quality, nipple type, etc. Some things in building "fast" wheels can even be counter intuitive, sometimes higher spoke counts can actually help you go faster by wasting less energy in flexing the wheels rather than propelling them forward, deeper wheels may be more aero but there is a threshold you can cross where you are just adding weight for the climbs slowing you more there than it helps in the faster sections. If you ride huge miles you may end up on wheels so stiff they beat you up so bad that you get fatigued from a harsh ride well before your legs are finished. This can be especially true with big gravel and dirt road rides that have a ton of washboard more than on pavement.
The real art in custom wheels is not the black magic many think it is. It really comes down to paying attention to details many consider silly or trivial. Not only the obvious things like sufficient and even spoke tension, proper stress relieving, and proper lubrication of spoke threads but also other details like proper component selection for your riding style. Not only does that mean rims and hubs that fit your needs but also selecting the right spokes and nipples for your rim selection. Some rims can not handle the extra stiffness from heavier gauge spokes but will work flawlessly with lighter gauge options, some combinations leave rear non drive side spokes at lower tensions than ideal and can benefit from lighter gauge spokes that seem to be happier at lower tensions on the non drive side. When durability is king, you can gain a ton of fatigue resistance by going with a triple butted spoke such as the DT Alpine 3. The number of options are truly limitless and this is why it pays to work with someone who has not only the experience to guide you through the component selection process but also the desire to do everything possible to exceed your expectations.
Sure, custom wheels can cost more than some of the bargains you can find in some online retailers but when you consider that wheels have one of the biggest impacts on ride quality and performance it seems like a silly place to cut corners, there is a reason pro teams have trucks filled with different options. With wheels, you also have to consider many people move their wheels from bike to bike, which makes them an even better long term investment. If you go with a builder who really takes pride in their work (like me) you will usually even get a lifetime guarantee against spoke breakage and free touch up work for life at no additional charge (who charges extra for them to stand behind their work anyways?!?!?).
Again, obviously I am very biased but after having built many thousands of wheels I have still not had a single person regret their decision to go with quality wheels tailored directly to their riding style. You give a lot of your life to this wonderful sport, indulge a little!