Ahhh...but you're missing the point of most of those combinations, which is to create skills that it makes sense for adventurers to take. Also, saying that they're separate things is of course true but so is hiding and moving silently.
The idea is thematic link and usefulness to a character. I can swim but I'm a lousy jumper and a mediocre climber. How would I represent this with grouped skills? I wouldn't. Can combining them help make the system more enjoyable? It could.
On specifics:
Arcana - Spellcraft does one thing...and I can honestly say that the only time I as a player (or one of my players when I DM) make a check for it is when told to by the DM. I can understand keeping UMD out though.
Decipher Script - Forgery is a non-skill. The chances of it being needed are few and far between and it is not one I've ever seen people jump at taking.
Use rope - this is an awkward one. I don't like it as a skill and I don't think it fits naturally with one area over another. Disable device (to handle the string components), craft (weaving, trapmaking), survival, Ride, Profession (sailor, teamster, etc).
Intuition - No animals aren't people but people are animals. If you watch what humans do, you see that we follow many of the same patterns. I didn't want to lump it in with perception because I think that one would be too powerful. If you specialize in observing body language, tone, and attitude, you can deal well with animals or people. Note that it isn't influence (which should be separate) but simply understanding that would be affected by these skills.
Survival + Know (Geography) - Show me a well trained survivalist who cannot rapidly discern the lay of the land well enough to draw a rough map of where they've been and I'll eat my hat (okay I don't wear hats but you get the point). My point is, no one takes Know (geog) unless a) they are taking all the knowledges, or b) they are a ranger and feel like they have to. Also, Know (Geog) grants a synergy bonus to survival.
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