Fullscreen apps stealing the window/focus on startup
Yes, this is annoying! Many forum posts mention the fix done by

defaults write com.apple.Dock workspaces-auto-swoosh -bool NO


with restarting the Dock afterwards:

killall Dock


This, however, didn't work for my Yosemite 10.10.2 installation. Just thought I mention it here until some real answer comes.

One of many sources.