Think about the possibility of massive attacks on locations. Saya group of clans/regiments come together and invade a part of let's say Venus. I'm not sure how many people can be in a single area but if there is controllable ship travel then events like this would be awsome.
Well, in order for this to work, Bungie would have to design the space for it, and I really don't see much call for dozens of Guardians coming together at an appointed time to do a single thing together. Maybe they could have really big public events, and you could get everyone into a public space and wait for it to happen, but other than that I don't really see the point.
Also, controllable ship travel is probably not a thing.