The simplified version of flashing is this: Plug in your laptop to your factory ECU to adjust settings and parameters to gain power and performance over factory tuning settings. Advantages - go faster, increase fuel economy (if thats what you tune for), add additional gain to supporting mods, etc.
Disadvantages - You need to know what the hell you are doing or else you are going to screw something up.

Now, lots and LOTS of places exist to show you "how to tune" using freeware. The only problem is they are not usually places filled with pro's giving out their tuning secrets and know-how. In fact, the pros are usually far far away from places like that because there are too many people giving out this kind of info. There are a lot of "Wiki-tuners" and "You-Tuners" out there that say they know what they are doing after watching a 5 minute video and reading over a forum. That's dangerous. Being "taught" by one of those places, or one of those people would be a huge disadvantage.

I'm not going to suggest that it is anything but very complicated for the average enthusiast to swap over the ECU. The entire harness will need to be swapped, the ignition system needs to be converted and configured for DIS (whether using dumb coils with a separate TU, or COP units with built in TU), the TB and IAC system needs to be switched over to something more compatible (or a retrofit needs to be configured), and half a dozen other patches and tweaks need to be made. There are differences, but I would suggest experience in knowing the systems and their functions would be required to pull off such a swap.

I don't want to discourage anyone from figuring this out on their own, but there is a reason why I haven't just thrown out all the info for everyone to see and try.