Summary: Lists provide more agency, while trees provide more easily anticipated results that are simpler to balance and utilize in design.
To be as concise as possible, the difference between lists and trees of decisions is the level of freedom the individual making the choices has.
When speaking of skills and character progression specifically, lists such as found in Elder Scrolls provide freeform decision making. Trees provide a more guided approach, usually representing classes or sub-classes of some form. There is less freedom in character progression/creation, as the concept of a tree necessitates requirements to unlock latter levels/branches.
The freeform list provides a greater sense of agency for the player, allowing a greater number of options. The more guided tree provides a simpler system to consider and anticipate as a designer, resulting in a system easier to balance. So, the end result is that you have a choice for a potentially more balanced system versus a system that provides more agency.
To answer your edit questions:
Complexity largely depends on the specifics of implementation. However, all else being equal, a freeform system is far more complex as the potential number of results are significantly higher.
Yes, the traditional usage of the two is for lists to be atomic actions (such as Elder Scrolls' system) while trees are used for "Perks" or "Abilities" to simulate a focus on developing enhanced skills in a specific domain. However, this is hardly a requirement.
Much changed between Morrowind and Skyrim, largely due to a number of decisions far too complex to attribute simply to "using a list-based skill system".