A friend of mine has been playing a scout through the Shackled City campaign (though with a number of levels of diviner as well) and I haven't seen any indication that the scout is not up to the rigors of 3.5 gaming. It's a class that's definitely not for someone who wants to stay in one place and get multiple attacks, though.
In the campaign I've running, the scout has been played up to level 16. Although the class is a solid class, I find it a little underpowered. An average scout is probably the match of an average rogue in many ways, but an optimized scout is easily outmatched by an optimized rogue. A few issues are the lack of UMD, getting skirmish only once a round and at fewer dice while sneak attack can often be had more than once per round, and the relative weakness of hide in plain sight and blindsense compared to defensive roll, crippling strike and so forth. They have some nice defenses, but as has oft been said, defense never won a war. In PF, they get the same benefit as the rogue in that fewer creatures are immune to precision damage, and suffer less from a lack of UMD since anyone can now train it and they have plenty of skill ranks.
In short, they could use a second look for PF, and probably need a slight boost.
What I would recommend for PF is:
Question 1
2) A high mobility skirmisher, a la Complete Adventurer
Ok. Skirmish attack is not my favorite mechanic (honestly, it gets silly after a while), but sure. I might consider continuing with this theme in some way.
Question 2
B) Trapfinding if you have to choose because it's a scout, not a hunter, though why not include both Trapfinding and Tracking?
The reason I ask is because it's easier for me to visualize a scout tracking ("Mangy Buffalo says many Frenchmen have come this way recently") versus somewhat difficult to visualize a scout disabling ancient runes and arrow traps in a hidden jungle temple (although possible - see, Indiana Jones).
Why not both? My good sir, it just isn't done. But seriously, I would like a new class to step on as few toes as possible, rather than as many, and there may be balance issues to consider when a class has very large bonuses in a number of skills. I just don't know about that, and how would you balance it?
Question 3
Much harder choice. I would consider keeping the bonus feats and perhaps including the Vital Strike feats automatically once the BAB is high enough as part of the class's power progression.
I actually looked at simply replacing skirmish with Vital Strike (for a precedent, see Monk and their access to Stunning Fist). However, I noticed several issues. First, Vital Strike has only two advances, and indeed, I would be cautious about handing out lots of dice that can be used as a standard action (although 3.5 warlock does it, and one version of my scout with medium BAB does it). Second, Vital strike is intended to scale with weapon damage, so that it is useful for fighters. However, scouts are normally armed with short bows, short swords, and handaxes, and as with rogues, it would be against archetype if their central mechanic encouraged them to seek proficiency with high damage weapons such as greatswords and exotic bows.
