The biggest thing you can do to improve the acoustic tone is to record it in stereo. They sound incredibly dull if you don't. Even if it's going to be deep in the mix, record in stereo anyway and don't pan it very wide. Always try flipping the phase on one of the tracks when you're done, and pick which sounds better.
It's hard to record acoustic without getting boominess. Obviously, don't aim toward the soundhole. I've been using an X/Y pair of mics directly in front of the soundhole, but pointed apart at 90-110 degree angles and back up until the mics "hit" the guitar at roughly an equalateral triangle. If it still sounds boomy, try pulling down the EQ around 200 hz. Condensor mics are definitely the weapon of choice for this - they give a more detailed sound. I've only got large diaphragms, but I've heard small diaphragms are very good for acoustic. Maybe someday I'll splurge.
You can also used spaced omnis for a different, more intimate and natural sound. You'll pick up more room noise, but since omnis don't have the proximity effect (gets boomier when you're near them), you can get them much closer.
I've got really crappy acoustics in my studio, so I got a giant piece of foam, maybe 7 foot by 4 foot and an inch thick. When I'm recording, I wrap it behind my chair to absorb some of the room ambience, which is usually not what I'm looking for. I hear a lot of acoustics here with too much ambience, and this might help.
If you're using a capo, especially high up on the fretboard, tie a sock around the other end of the fretboard to keep the resonance monsters from ruining your take. If you want to hear an all too good example of that, check out my SF version of "Can't Take Our Love Away". I re-recorded it for the album because the resonant buzz drove me nuts.
Also, acoustic guitar dynamics are a beast. Ideally, you'll almost need two ways of playing - normally, and in the studio. The goal is to need a minimal amount of compression. So pick a little lighter and more consistently. Banging away sounds great live, but it doesn't carry over into the studio very well.
Oh, and I swear by Elixirs. They're so good. And they have a studio benefit - the strings won't squeak when you slide across them. I usually have to compensate with adding a little brightness in the mix, but their overall natural tone is worth it.
Edit: And for gods sake, if you're going to use your guitar's pickup, keep it really low in the mix. I've only done this
once, using a little bit of low-passed pickup to really beef up the bass, but it was an interesting effect.