Even though we make Sococo, we had to train our management to ONLY do Sococo conferences for exactly the reasons you mention. Everything went much faster after that.
In fact we have to train them to stop calling it a 'conference call'. Its just a meeting, like any other meeting you ever held before. Except everyone can hear everyone perfectly; more than one person can share docs (at the same time!) and everyone can keep in sync effortlessly.
Whenever possible we prefer everyone be connected individually as opposed to sitting together in a conference room. The conference room becomes a distraction, impedes proper communication between all members and the attention spans increased when everyone connects from their workstation. The conference room creates two areas with two distinct conversations so if we're really aiming for an integrated environment we enforce people connecting from their workstations as opposed to using a conference room.
Culturally it also spreads that idea that those sitting together are better than the remote workers, which given our line of work is an unproductive idea to keep propagating. And while there might be differences, they pale in comparison to the negative impact that ignoring or discriminating remote workers has in our projects.