1. 5 skills with +9 distributed should be the cap, and should be unusual.
3 / +5 or +6 -> typical characters in classes that have 2+Int
3 or 4 / +6 to +7 -> most characters
4 or 5 / +7 to +8 -> characters in classes that have 6 or 8+Int
5 / +9 -> very exceptional characters.
2. There isn't a correlation, though d12+3 is something better avoided. There are actual characters (Enora, Feiya, Siwar) that have a d12+3 skill, but should be considered exceptional.
3. Yes, though it's more for subskills. Survival, Fortitude, and Craft are key subskills in S&S, while Knowledge is key in Wrath. Combat skills (Melee, Ranged, Arcane, Divine) are valuable in all sets.
Just rifle through boon and bane decks to see how often different skills come up, and you'll get a feel for which skills are key.
Enora has Arcane +1, Craft +1, and Knowledge +3 under Int - and nothing else; she pays for her d12+3 by being a 3/+5 and having no strong "on-character" solution vs. banes until she gets her role card.
Wrath Knowledge aside, intelligence is arguably the weakest of the six stats. Consider what the stats do. Subskills listed are typical, not absolute (eg, I don't list Ranged for Strength, even though Imrijka has that.)
Str: (Melee)
Checks involving melee weapons, default combat check.
Dex: (Ranged, Disable, Stealth, Acrobatics; some characters have a Finesse power for Melee)
(Ranged) Checks involving ranged weapons
(Melee) Checks involving melee weapons that have Finesse
(Acrobatics) Checks against some "before you act" damage
(Disable) Common against barriers
Con: (Fortitude)
Checks against effects that bury cards from your deck (!!), checks to acquire armour.
Int: (Arcane, Knowledge, Craft)
(Arcane) Checks involving Arcane spells
(Craft) Checks to acquire potions, (S&S) firearms which can also be acquired on Dex/Ranged, and (S&S) to repair your ship.
(Knowledge, Wrath) Checks to expose monster weaknesses, and acquire books.
Wis: (Divine, Perception, Survival)
(Divine) Checks involving Divine spells, checks to acquire blessings.
(Survival) Checks to acquire Animal allies, (S&S) checks against ships.
Cha: (Arcane, Divine, Diplomacy)
(Diplomacy) Checks to acquire Humanoid allies.
Sandslice covered everything well, so I don't have much more to add, but I will say a couple rules of thumb I have:
1. There are certain skills that should be valued more highly than others, just based on their general usefulness. The big ones are Melee, Ranged, Arcane and Divine, which are universally useful in multiple ways (Most importantly, they are the skills that readily translate into combat checks), and therefore generally cost a bit more than other skills. Also, just because a set values a secondary skill mroe highly (see survival in S&S), that does not mean it should be costed more on the card. Survival should be considered the same on a character designed for S&S as one designed for WotR. This does 2 things: 1. it means that the character that has Survival in S&S can feel special, since they are specifically prepared for it, so a power-gamer can feel rewarded for their forward thinking, and 2. it allows a character to be transferred between campaigns with less risk of power fluctuations. If Survival is normally weighted as equal to Diplomacy in RotR, but equal to Divine in S&S, then if you take a character with survival from RotR and put it in S&S, they will be overpowered compared to characters with survival from that set.
2. I think that the die of the skill that a secondary skill is attached to does affect the cost. If you have a larger base skill, then having a secondary skill attached to it is just stronger. I don't know if there is a formula (I think it's more a feel and testing thing), but when you are comparing your character to existing ones, keep in mind that the same skills on bigger dice will normally be more powerful. (The most obvious example I can think of is RotR Valeros and Kyra. Both have Melee+3. But with a d10, Valeros is considered one of the best melee characters, while with a d6, Kyra is considered barely passable at melee.)