Many of the issues in building in microgravity are based on lack of experience and a large enough database for quality control. As well, there are time and distance issues (for example, if you have a defective part on Earth, FedEX can deliver a replacement the next day, while waiting for SpaceX to get a launch ready will take several days at best, but more likely weeks or even months).
For the near and possibly mid future, the best way to overcome these issues is to build modules in a factory on Earth, and then assemble completed modular units in orbit, much like the ISS was assembled. There are other historical analogies, the Type XXI U boats built near the end of WWII were built from modular assemblies sent by rail to the shipyard for final assembly, for example.
Even in the Plausible Mid Future, assembly of modules might be done in pressurized bays on the Moon and then sent into space via mass driver, or an asteroid could be hollowed out and spun for gravity and a pressurized bay for building and checkout will be used. A pressurized bay in microgravity may be used, if you are willing to put up with microgravity issues. Robots might (and indeed probably will) do the bulk of the work, but a pressurized bay allows a human quality control inspector easy access and the ability to get in without the restrictions of a spacesuit.
Based on this, future spacecraft and stations might resemble cylinders of various size attached to a central truss work. With construction bays in hollowed out asteroids, the modules could be of pretty impressive size.
As an alternative, for very large construction, a "balloon" could be inflated and pressurized, and construction done inside. The balloon will become the outer hull of whatever you are building, and all the other stuff you need built inside in the comfort of a pressurized environment. A variation of this idea is on the Neofuel site, which uses a rotating balloon filled with ice to form the structure, and the various structural elements built inside: http://www.neofuel.com/iceship/index.html
So in general, the progression will be to build modules on Earth for on orbit construction, then migrate to the Moon to mine materials and then build modular sections, moving to asteroids to make modules until we finally build large enclosures to define the outline of the spacecraft/structure and build the structures inside.
Grab some tools and get busy.