It is to prevent superskills.
I was only commenting on the name, superskills must be avoided at all costs, or the list gets too short and the result is being too close to just using the 6 abilities, which makes skills distinction pointless.
I know I suggested to lump Search into Perception, but actually what should be done instead is expand Search into
Investigation and add more uses (e.g. not only searching for hidden objects but perhaps searching for immaterial clues, and why not searching for people in a city and information in a library?).
We should avoid the temptation of merging skills just because we want our PC to be more powerful. As you say, if we take a look at the list and assume a PC can pick 3 skills, there are clearly some dominant ones like Athletics and Acrobatics which will be taken by pretty much every martial character:
Acrobatics (Dex)
Animal Handling (Wis)
Arcana (Int)
Athletics (Str)
Deception (Cha)
History (Int)
Intimidation (Cha)
Medicine (Int)
Nature (Int)
Perception (Wis)
Performance (Cha)
Persuasion (Cha)
Religion (Int)
Search (Int)
Sense Motive (Wis)
Sleight of Hand (Dex)
Stealth (Dex)
Survival (Wis)
They are still quite few. We need more Str-based skills at least, but which ones? Break an object really didn't make any sense to me.
OTOH there is a good way out... it all depends on whether skills and proficiencies (and possibly also languages) are in the same "pool". If they are, then we're good to go with this list, because you could choose a proficiency or a language in place of a skill so the real list is much longer.
However I'd really like to see some
Alchemy and
Herbalism back into the game. They don't have to be skills strictly, they can be proficiencies, but I'd like them into the same pool.
Another good addition would be
Appraise (tho it needs to be expanded because the 3e version really is too narrow), although it was practically there as Trade Lore, even tho that requires a specific subfield. Actually,
professions (or trade lores, whatever they are called) should be there somewhere. I think they are a both a great tool for character building, and a good example of a skill that uses different abilities depending on the check, e.g. a master Trapsmith would make Int checks when designing new traps, Dex checks when crafting them, Wis checks when studying an existing trap or assessing the value, Cha checks when dealing with suppliers and customers...
Also we need a skill or proficiency in
Devices, currently we have Thieves' Tools proficiency for traps and locks, but how about tinkerers and mechanics? This could however be absent in the core game and added later for specific campaign settings.
Finally a word about
Riding: I am not sure this is better as a proficiency, perhaps it should be back as a skill, or it should be both at the same time. Checks are still needed in difficult situations, such as when trying to cross a river while on a horse, pursuing a target, not get stuck in a swamp, control a frightened horse etc, so this suggests it would be fine as a skill. OTOH it's also good to set some requirements for special mounts. I am not sure if it's better to assume everyone can ride a regular horse or only those proficient, but otherwise better mounts (warhorses, monstrous mounts, and of course flying mounts) are probably better restricted to proficient characters only (unless the mount is intelligent to drive by itself).