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You know I see a lot of people bashing STO for the heavy use of instancing but I would like to address that from a Star Trek point of view.
Of all the Star Trek episodes what percentage would you say does the Enterprise, Defiant or Voyager have a fleet with it? I would say it would be a safe bet the number would be less than 10%. The vastness of space and the need to cover so much area and exploration necessitates that the ships and thier crews be able to operate for extended periods of time solo.
Take this even a step further, when a ship in the show needed help it was typically hours away and they seldom had a choice at what kind of ship would respond.
Now I am not saying it was a pruposeful design decision but I am saying that it actually goes to capturing the feel of Star Trek.
I have a soap box and I am not afraid to use it.