Companies look for three things when they decide where to be located: cheap rents, strong economy, and large workforce. Right now, the South fits that formula. Everyone is moving there because of the "nice" weather and cheaper housing. Consequently, many northern cities are suffering (yes, even those with some skyscrapers). Contrary to what you believe, Boston is actually pretty well off. There is a growing demand for office space and the lowest vacancy rate in years, and all of that can be traced to quality of life. People love the human-scale urbanity of Boston, educational resources, abundant greenspace, and high culture. The only thing keeping people from moving here in droves are the outrageous housing costs. Sooo, that brings us back to Fan Pier. If developers continue building condos and apartments, prices will be forced to go down. Eventually, as prices get more affordable, more of the hundreds of thousands of college graduates in the area will decide to stay in Boston. Companies will look to Boston and be willing to pay high rents to tap into the educated labor pool. Then we can build your beloved skyscrapers to house new companies.
While skyscrapers are a plus, they are in no way "the reason" companies move to a city. It's really quite simple: quality of life attracts people, which attract companies. The only thing Boston is missing is cheaper housing.