I guess that skills which are truly complementary ought to be merged together. By complementary, I mean two (or more) skills which inseparably go together within a given adventuring niche (such as thievery) and which most characters occupying that niche (such as rogues) will want to pump up said skills at the same rate because it would be a significant disadvantage for them *not* to do so. Hide and Move Silently are an iconic example of this.
For any two skills that could be merged, would it harm the character to max out in one and not the other if that is part of their "shtick"? For Craft and Appraise I would say no. Appraise will get you a lot more in terms of benefits, while Craft is almost a throwaway skill unless your GM likes to break your stuff or keeps you away from civilization for months at a time. Climb and Swim? Not really inseparable either, unless you are a pirate. Ride and Fly? Definitely not inseparable, and Fly doesn't even matter without a means of flight. Bluff and Disguise? If your chosen profession is spy you might depend on the two simultaneously, but you can generally get along with a high Bluff if that's your thing, without also needing to commit identity theft.
From D&D 3.0 to D&D 3.5 and then to Pathfinder, some consolidation of skills was interesting, helpful, and even efficient, but I would recommend against trying consolidation as some whizbang great idea that will surely make skills make more sense somehow, or for no other purpose than just to simplify the skill system for simplification's sake. There needs to be a better reason to merge two skills other than "they go together thematically for some characters." 3E's Alchemy was really a Craft skill in disguise, so it needed to be put right. Hide/Move Silently was a split that, while it mimicked the division between Listen and Spot and looked good on paper, was unnecessary and hurt rogues by soaking up more skill points when they didn't have to. The whole idea of "exclusive skills" scremed "I need to be a class feature instead!" And Intuit Direction, Innuendo, and Read Lips were such specialized tasks that they were a waste of ranks and it would take a GM/DM to have a cruelty streak to want to make it necessary to be good in one of these skills as a plot twist, knowing no one in the party would ever spend the points on them. Concentration technically wasn't "merged" per se, but it was a skill that was either useless if you weren't a caster, or was absolutely vital if you were one--so it got converted into a sort-of-but-not-really class ability that every caster could max out in all the time.
I don't really like that Perception is almost a must-have skill for every character in the game, but if we still had Spot, Listen, and Search as separate skills in Pathfinder, we would probably still be seeing every character who cared about noticing things pumping them up at roughly the same rate. Indirectly, the division between Spot, Search, and Listen could represent a higher cost for being good at noticing things, because you would have to pump them all up at extra expense to be really all-around good at perception, but then you could try to save a few skill points/ranks and just specialize in one over the other two--but I don't know how often such a strategy was used with thiefy/sneaky characters in D&D 3.X.
IMO, skills which are "really good to have" or which represent certain iconic behaviors in fantasy gaming ought to have extra emphasis by being broken down into specialties. This is one reason why we shouldn't have a single, all-encompassing Knowledge skill, or a single "physical movement" skill instead of Acrobatics, Climb, and Swim (four if you include Fly), or a single social manipulation skill instead of Bluff, Diplomacy, and Intimidate. There's also a needful split between Spellcraft, Knowledge (arcana), and Use Magic Device. Toying around with Things Not Meant For You (tm) is what UMD is all about and it would be a loss to the game's flavor to mash that up with the other two 'magical arts' skills, whereas Knowledge: arcana represents more general information about the mysteries of the unnatural world, and Spellcraft is about spellcasting and magic items.