Rather then merging skills there are almost enough groupings of skills to want to create columns of related skills, putting all the physical skills in one (guns, weapons, fists, athletics, endurance), social in one (intimidate, deceit, rapport, empathy, presence), and then group the remaining 15 skills into a few groups like maybe (discipline, conviction, lore, scholarship) and ( stealth, burglary, investigation, alertness) et al.
Then restrict a player to using only one skill column on their skill tree ( meaning only one grouped skill in any one skill rank). This sort of thing starts to create a more rounded characters but still gives most of the variety that you would want from a diverse skill choice without having goons who cant talk and talkers who just stand there and bleed. Heck you could even give out more skill points so people are missing less skills but make each column one rank lower then the previous to create a very sloped sort of organization. You end up with less skills (and trappings) missed while not having to monkey odd trappings together as much.
PS: if your finding athletics to be far to potent, then yank the dodge trapping out, put a 'taking cover' trapping in guns to count as ranged defense, and 'spell defense' into discipline, and then everyone defends like skill with like skill, and then bringing a knife to a gun fight is way stronger truism.