That's a hot one! Here are some things I like about cages for my situation:
I like seeing my rabbits content in their cages, happy to have their own area and unconcerned about the possibility of intruders. That said, I have had a few squabbles in cages with grow outs as they got up to 5-6lbs. My rabbits (Rex) do not seem like they would do especially well in a colony. They can be opinionated and energetic, and I could foresee too much fighting.
(Side note: have you seen a domestic turkey hen fight with wild turkey hens?! They slap each other with their wings, make threatening sounds at each other and all kinds of stuff! Our hen did not want to allow any others in her area. )
I like not having my rabbits exposed to whatever I bring in on my boots from other animals, like could happen in a colony. This is a big one for me.
Although cages can cost a lot (I spent a ton on them this year), I personally need to make better use of my building's space by using cages, rather than only having a few breeders on the floor.
I like being able to monitor individual rabbits and catch them easily without stressing them much. There are ways to deal with that in colonies, though.
I use a deep-bedding method for chickens using pine wood shavings (have also used straw at times). I don't think I could stand using that method for as many rabbits as I need to raise, although, if I only had a couple in an oversized area, I think I could be fine with it.
Since the manure is going to be used in my garden, I don't like having wood shavings in it. I read somewhere that wood shavings pull nitrogen out of the soil around them as they decompose, thus making less nitrogen available to the plants. I want to be able to put the manure straight into the garden and not have to compost it like other manures.
Parasites can be a difficult issue in colonies, obviously depending on the way it it set up and how they are fed, etc. It can be very difficult to get rid of them once they are in the soil/area. The same can be true for wooden hutches, though.
For me, it is just simpler to not have to monitor and fine-tune a colony.
Now that I put all that out there- I know others have awesome perspectives and experience with both methods, too. There are some pretty ingenious ways to do things out there!