Well, one idea I had, for example, is that the Second Shivan incursion proved that if theres one thing the GTVA are lacking in, it's the ability to empty ships quickly in emergency situations. The GTVA's current arsenal of support and evacuation ships are too thinly armoured and lacking in capacity to do anything more than hopefully effect a repair or remove the command crew. Secondly, the NTF insurgence suggests there may be a future need to deploy troops far faster than previously, and under heavier combat conditions. The solution would be something about 3/4 of the size of a Fenris, with limited weapons but good speed and thick armor. The ship could deliver troops in large numbers during combat, allowing faster and more effective over-running of an objective. Also, because of it's large accomodative ability, in emergency situations such a ship could take the large percentage of the entire crew of a Deimos, in admittedly cramped conditions, thus saving on the GTVA's fastest dwindling asset, personnel.[/non-canon)
It's not precisely 'Special Ops', but it performs a pretty specific role...