All of these worlds are yours…
As I mentioned in my section on the arks that brought colonists to the 'Verse, the arks were designed to be broken up for use after arrival. The massive engine sections were used to move comets around for the purposes of bombarding planets to increase their atmospheres and water. Atmosphere processors were installed to convert unbreathable atmospheres to something humans could tolerate and cloned plants and animals assisted the process. Terraforming is still going on today, according to the episode "Shindig", where Mal is talking with some slave traders in the pool hall.

But it seems like there are a lot of marginal, barely populated worlds in the 'Verse. With a wide variety of worlds, why were these worlds terraformed at all? Just looking at the TV show and movie, we have worlds like Whitefall, Regina, Lilac and Whittier that are dry, desolate and sparsely populated.

Where is everyone?
So I tried to think of some reasons these worlds seem sparsely populated:
1. Maybe we only saw the outback of these worlds and there are larger cities elsewhere. That seems unlikely. In the TV show, people like Patience, Magistrate Higgins and Russ Burgess rule their worlds and they certainly aren't living in well settled areas.
2. No one wanted to move. Alliance propaganda during the war painted the Rim as unpleasant, so it backfired and reduced interest in immigrating to the Rim. People still do, but they seem to be small, group efforts, not government sponsored.
3. Economic disruption. With the issues from the war, maybe there wasn't the capital to finance colonization efforts.
4. Loss of colonial transports at Miranda. When the reavers were created, ships at Miranda were lost with their crews. The loss of those vessels may have hampered further transportation of colonists.
5. Alliance policy turned against colonization. Reducing immigration keeps core world populations high, maintaining their political supremacy and reducing the manpower pool for any future rebellions to draw on.

The Dressler Report
The Big Damn Heroes Handbook introduces The Dressler Report, a secret document that predicts that the Alliance government is going to collapse due to excessive growth, the same section also talks about the financial difficulties of supporting current terraforming efforts on worlds which are harder to convert. Terraforming efforts are losing support and financial backing and taking longer.

Having said all that, why were they trying to terraform more worlds if they're not needed? I can see a couple of reasons. One might be a sort of "manifest destiny" thinking that the people of the 'Verse feel that they must convert all worlds that can be made habitable, so they will have room in the future. Another good possibility is simple bureaucratic empire building. I had suggested the Terraforming Commission to explain how terraforming was carried out. Well, when terraforming ends, their jobs are over. Maybe the Terraforming Commission is pushing for more terraforming to keep money coming into their pockets. And their corporate friends who make money supplying terraforming teams.

"Terraformers got a prodigious death rate"
This line is from one of the slave traders that sold people to terraforming groups. It has never made sense to me. When I think about terraforming, I think of space tugs dropping comets on planets, construction crews building giant atmosphere processors and biologists spreading genetically engineered plants and plankton to convert carbon dioxide to free oxygen. None of that sounds like unskilled slave labor.
Then I remembered a scene from Lois Bujold's novel "Memory". The main character lives on a partially terraformed world, most of which is still covered with native vegetation. He flies over a terraforming crew, doing it the old fashioned way: by slash and burn agriculture. Native plants are cut down and left to dry, then burned. The ash fertilizes the soil so Earth crops can be planted.
That's where slave labor comes into terraforming in the 'Verse. Once a planet is almost ready, it is seeded with genetically engineered plants, probably trees, which help convert the atmosphere. Then logging crews cut them down and let them dry, then forest fires are set to burn the trees to ash and enrich the soil. Other plants may then be seeded onto the soil and plowed under when the first true crops go in.

On the issue of providing water to worlds being terraformed, this illustration shows how (relatively) little water there is on Earth. The worlds of the 'Verse are generally smaller and much drier, so even less water would be needed.