1.) Data Centers are expensive to operate. Over estimating could cost a company
hundreds of thousands of dollars in unnecessary costs.
2.) Data Centers are time consuming to expand. It's not as simple as installing Windows 7 on your desktop. You need to prepare hundreds of discrete operators, and then link them together, and then link that cluster to the larger server network.
This takes a lot of time.
Should there have been more server capacity? Yes, but it's too easy to say that now when it's needed. But a cursory look at the load issues show pretty clearly that they started about two days after the game went live. Square probably noticed that they were approaching their limits during early access, and were working to get new clusters spinning since then. But again, this isn't a "call up godaddy" situation.
Look I'm annoyed, too. I'm betting my return to MMO gaming on FFXIV, and I was massively impressed by what I saw in beta. But a little maturity goes a long way here.