I've done a few painted kayaks. Paint can be a great finish for a kayak. Hopefully I can help answer your questions.

Do I need to completely fill the weave of the new glass job or will the 2-3 coats of paint finish it for me?

It depends on how fussy you want to be. Skin on frames are finished with paint and the weave of the cloth can still be felt through the layers of paint. In theory you could do the same. You may lose a bit of strength doing so. For a very smooth finish you should fill the weave completely. Paint, being uniform in hue, will show EVERY ripple, pin hole and other flaw. Luckily you don't need to use straight, neat epoxy to fill the weave. Adding some microballoons can help sanding.

Does paint last longer than varnish as far as scheduled maintenance?

Yes. A good, high-quality marine urethane will last for many, many seasons before needing any recoating. A good urethane could theoretically last the lifetime of the kayak. Being opaque, it has much higher UV protection than any varnish. For abrasion, it depends on the paint but a single component paint is softer than two-pot urethanes and abrade quicker. That said single component paint (like Interlux Brightsides) is about the same as varnish. The good thing is scratches usually aren't as noticeable with paint.

On the hull of my recent BTD Panthera I'm trying a silicone-epoxy paint called "Wetlander." It's very slippery, flexible and tough. It's also waterborne so the cleanup is easy. It's most often used on the bottom of airboats. I've had it out a few time now and it's been quite impressive. It'll be interesting to see how it lasts over the next few seasons.

Will a dark color hide scratches better?

It depends on the paint system but, generally, no. Scratches usually show up lighter than the paint (like with varnish). If you use a clear coat (eg automotive systems) the scratches will be mostly in the clear coat and will turn white. Its not as obvious with solid paint systems (like Brightsides). If the paint is thick enough (on the lines of gel-coat) darker colors can work. The best color for hiding scratches though is white.

If you are thinking of painting your kayak consider also tinting the epoxy fill coats (and seal coat if you use one). Scratches will be even less obvious if the underlying epoxy is a similar color. I would wet out the fiberglass cloth with un-tinted epoxy though. It'll be much easier to gauge the wet out.