The following are a few of the many factors to consider:

Roof Pitch: If for climate or architectural reasons you need a sloped roof, a vegetated roof is less likely. Sloped roofs are also typically visible to passersby, so aesthetics are more of a consideration.   
Energy and comfort: The heat island effect is more of a problem in urban environments with long stretches of hot weather. If your project is in such a location, this credit might be a higher priority from a comfort and energy perspective. Light-colored and vegetated roofs reflect sunlight, thus lowering cooling bills. Green roofs also add insulation value to roofs, helping prevent both heat gain and heat loss. 
Climate and water: Does your site's climate support the use of a green roof? Will a vegetated roof require permanent irrigation? How does roof impact overall water balance of the site? Does your site need to control stormwater runoff?  Would a green roof help achieve stormwater runoff goals?
Structure: Does your project building have sufficient structural support for a green roof?  
Glare: Particularly for pitched roofs, consider impact of reflective or light-colored roofing on surrounding buildings and roadways. A glare study may be helpful in some cases.
Views: Often a green roof can enhance views compared with conventional roofing.
Maintenance: Light-colored roofs will benefit from periodic cleaning to maintain their reflectivity. Green roofs will need some level of landscape maintenance depending on the type of vegetation installed.