well with canned tunes, they have to be real conservative so that it is safe on every single car that it could be put on to, you never know what kind of condition the car may be in (weak fuel pump for instance could be a major problem that might not show up until tuned) not to mention that most of them could be put on 100% stock cars, a real tuner can take any and all mods into consideration, or configure it for special request.
also there is not a whole lot of power that can be freed up with the tune, most of the difference is from the trans tuning, which again is better when done by somebody that actually has hands on experience with the LS.
also, if you ever have any issues with the tune (which a lot of people have for many many different reasons) you can data log and send it back to the real tuner and have adjustments made.
as far as "another couple hundred of dollars" on top of the tuner price, a lot of guys will cut a discount if you buy the tuner and the tunes from the same guy, years ago when my cousin had a former tuner on here do his car, he got the tuner and two or three tunes pre-loaded and shipped for just a few bucks more that what it could be had for online.
and if you really want it done right, you can not beat a dyno tune, this option will be the most expensive, but will allow you to squeeze as much as possible out of your car, and will help to discover any issues your car may be having.
