#1
Which is best for sound?
Buying an electro acoustic?
Or Buying a standard acoustic and installing a pickup on it?

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#2
I tend to disagree with the poster above. I think you can achieve a much better sound both acoustically and amplified if you choose and acoustic and then choose a pickup to have installed. It really is just all about how much money you can spend though.
#3
I'm with jim on this one. Adding aftermarket pickups means that you have more options in the future. Here are some advantages of buying aftermarket:
1. The systems are usually quite discrete--You don't have a HUGE hole cut in the side of your guitar
2. You can choose the type of electronics you want--internal mic? magnetic sound hole pickup? transducer? piezo? You don't get this kind of choice with buying onboard electronics
3. You don't have to get a cutaway--I have no use for a cutaway. I think they're ugly, too. But if I buy on board electronics, I'm getting a cutaway.
4. You can upgrade electronics in the future--If I buy an expensive guitar, I'm going to want the ability to upgrade electronics in the future to compliment my expensive guitar.
5. Manufacturers sometimes rip you off for electronics. Big time.

Of course there are downsides to aftermarket as well, and on boards have their own advantages too. Aftermarket has more advantages though, imo.
Equipment:
- Art & Lutherie Cedar CW (SOLD! )
- Martin D-16RGT w/ LR Baggs M1 Active Soundhole Pickup
- Seagull 25th Anniversary Flame Maple w/ LR Baggs Micro EQ

Have an acoustic guitar? Don't let your guitar dry out! Click here.
#4
Granted, it will likely be cheaper to buy the package, but agreed.
You have so much more of an option in the sound. Just make sure you do your research first!
My Rig:
Schecter 006 Diamond Series (Discontinued) Flat Black
Jackson JS30RR Metallic Blue
Line 6 Spider II 210
Boss TU-2
Sennheiser E835-S

Current Top 3:
Between the Buried and Me (Always)
The Faceless
Murder By Death