It is a joint structure. The upgrades effect your whole team. There are none that affect only you. Once someone upgrades something in the Citadel, that particular upgrade will be unavailable, but you will be able to buy the next upgrade, or another one.

Most people spend their money on equipment upgrades, and don't bother with the citadel upgrades though. Especially in random games.

The citadel upgrades have been sorely underestimated, especially for larger maps. There's a problem though in that those getting the most gold tend to be those that invest in personal stats. I'm trying to find a balance between both.