AOSP ROMs aren't allowed to include Gapps because Gapps are proprietary Google apps. They're not open source, and they're not part of AOSP. It is illegal to use Google's IP (Gapps) without permission. They get around the restriction by making you download and flash the Gapps separately. Gapps are included in Touchwiz ROMs because Touchwiz ROMs are just modifications of the manufacturer's ROM, which already has the rights to use Gapps.
In September 2009, Steve Kondik (Cyanogen of the CyanogenMod team) received a cease and desist letter from Google, demanding that the Google Apps not be included in the team's ROMs, since the ROM could be ported to devices which are not licensed to have the Google Apps. In turn, that would bypass the requirement for the devices to be licensed. For a few days, development on the ROM ceased, there were outcries from Android users all over the Internet, and many bloggers suspected Google had just shot itself in the foot.
Eventually, an alternate method was found, whereby Google Apps are not included in the ROM proper but the Google Apps which came with a device would be backed up by the device's custom recovery or another app, and then re-installed onto the device once the new ROM was flashed. This would therefore "Google-ify" one's ROM.
In order to update the Google Apps for devices which have not been updated to the latest versions of Android, and to simplify the Google Apps installation process, the Google Apps are now traditionally packaged in a separate flashable ZIP which can be easily installed on top of a ROM. This allows for faster installations, easier upgrades of Google software, less tasks for the custom recovery to perform, more user-friendly installations, and an overall more streamlined process.
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