Great ideas. A few notes. Instead of terraforming the entire planet, which would take a very long time, and sending hard shell habitat capsules,*1 which would drive its inhabitants crazy in short time due to the lack of space, i suggest the habitat modules should be inflatable and made with transparent materials for light.
This inflatable habitat modules will contain lighting, water/gas piping, mist generators, wind fans, nutrient/seed delivery, and other climate control and life support systems installed. This would give much bigger space to work with at a fraction of weight, resulting in bigger payload. The remotely controlled drones can be utilized for sampling, maintenance, and monitoring.
Next, a soil sample from inside the dome will tell what mineral distribution is within the soil and the availability of the necessary for life minerals, such as potassium etc, then the automated system will replenish the missing minerals by specially designed delivery methods, i.e. rotating disk spreading the mineral powders from a set of containers that can be opened and closed automatically.
Once the mineral base is established then the micro bacterial cultures will have to be introduced, which means planting fungi and compost materials that will break down the minerals to make it into a fertile soil which then can be used by the roots of thy plants, who in turn will start making oxygen from the plentiful carbon dioxide.
Then the animals can be introduced, such as the earth worms, pollinators (can be artificial), whatever the requirements for the functioning biosphere are, and then the astronauts can come by and fine tune it to the human needs.
"Once conditions become more suitable for life of the introduced species, the importation of microbial life could begin.[12] As conditions approach that of Earth, plant life could also be brought in. This would accelerate the production of oxygen, which theoretically would make the planet eventually able to support animal life."*2
Considering that the Martians and other aliens do not interfere, purely hypothetical scenario, since, presumably, the aliens are everywhere. I personally think the Martian military colony has been operational for close to fifty years if not longer. However, I am more interested in making the Earth a better home base, so much needs to be done here still. Although, who would refuse an opportunity to leave the planet and go on the interstellar adventure...
*1 - http://www.disclose.tv/action/viewvideo/187886/THE_SECRET_STORY_OF_PLANET_MARS__Documentary_2014/
*2 - http://en.wikipedia.org/wiki/Terraforming