I feel like shuttles as a whole are per unit more costly than rockets. Also more complicated, depending on if you have the one tank or multiple tanks. The upside is the experience of gliding it back, and also returning the boosters and/or tank(s), if that's your style. Also the lower stage count, as in separate parts staged, unless of course you have one main stage and then an orbital insertion stage. As a whole, both types of craft can be very flexible in design when it comes to KSP. For instance, recently I tried making a massive fuel shuttle design, where it had a main tank, and then some small tanks for fuel for orbital insertion. This was then mounted under basically a frame with wings, which would carry it aloft to a good 10km. This is a very complicated but rewarding craft design, in terms of recovering the parts. I have not gotten it to work yet, but I'm working on it. Also, an upside to shuttles is that if you want to bring something back down to Kerbin to a specific landing site, you can, granted that you have Kerbinside or good landing system.
One final downside of shuttles and spaceplanes is the lack of heat shielding parts compatible with the space plane line of parts. There's only heat shields, which don't look nice on wings. So they have to be a lot more micromanaged than rockets with heat shields. That's why I'm now planning on making a line of parts that can act as heat shields, only no ablative, carbon-ceramic heat tiles, for each fuselage type. The MK3 set would creat a flat bottom. Not sure about the other designs, just had the idea for it. It would be the first time I made any parts and tried to implement them, so it may take a bit.