I do think skill progressions are lame, most of the time; I think skill trees are beautiful and logical.
However why should players get to choose skills at all
Instead, racial and class selection should determine initial skills. Attribute bonuses should dictate initial skills learned above and beyond at PC creation...and that's it.
After that, it's improve by doing or training, with caps based on level progression. Certain class levels
require skill growth in order to advance (ex: thief classes). A skill tree allows for say proficiency in daggers to result in rollover ability in
-- other small sharp weapons incl axes, improvised (broken bottles, shards of whatever)
-- all sharp weapons incl swords of various sizes
-- one handed combat incl one handed blunt weapons, ranged weapons, various maneuvers, weapon maintenance etc
-- one handed tasks in general, including pick pocket if class allows it
-- physical tasks in general
Players should only be allowed to learn or do the very bottom of each skill tree. Skill growth in one node is capped; to maximize, need skill growth in others. so specializing in dagger is possible, but neglect other skills and dagger never goes above x%.
Certain skills that are common to everyone are more
talents and should not be part of the skill tree.
Talents should be driven by attributes, race, class selections and improve by level.
I also think that level progression should include both class (ex: thief)
and race (ex: dwarf), with special racial quests required for racial progression at appropriate intervals, with overall level and skill progression capped until the racial quests are completed. A racial quest would be something relevant to the racial culture of the PC--perhaps a dwarf has to return to a stronghold to pay a tithe to an elder in exchange for adventuring rights, or something else
expensive.