I agree that BWS should enable more user choice, not less. Hence recent changes allowing expert users to override BWS rules even in cases where ignoring those rules might have game breaking consequences. I also agree that most conflict rules should be based on technical incompatibility.
However BWS also has a concept of warning/notice rules for cases of conceptual incompatibility - where installing X and Y together means that the core intent of X is thwarted by Y or there will be obvious inconsistencies (for example if X contains dialogue written assuming that an
NPC is dead while Y prevents that
NPC from dying).
Another recent change of mine has resulted in BWS not automatically solving these conceptual incompatibility rules when users first load up the tool; instead the choice is presented to the user.
For non-"warning" rules, BWS does initially solve conflicts by only selecting one of the eligible mods/components for each rule. The priority goes to the first mod/component listed, so I have adopted the practice of moving the newest or most recently updated mods to the front of these rules to encourage more players to try them.
BWS also has the concept of pre-selections: minimal, recommended, maximized, tactical, expert. We tag individual mods and components in these categories to provide a predefined selection of enabled and disabled components, from which users can then further customize as much as they want. Recommended is a judgment about quality and how well a mod fits into the game. This is a bit fuzzy still, but it is just a recommendation. The other categories have no quality control at this point; the only consistent policy is that mods which fail to install or which break the game technically (requiring more than basic CLUA skills to resolve) are categorized as expert pending analysis and patching. No mod or component should be permanently in the expert category - it is a queue for known problems until we solve them.
BWS also has notes about mods and components describing known problems, compatibility considerations, etc. Some of this is taken from mod readmes, some from forum threads, and some from direct examination of mods' code. The intent is to be as accurate as possible and reports from users are constantly improving this aspect of BWS.
I hope this addresses your concerns; if not, happy to consider further suggestions for improvement.