The first mod I did (other than some Duck tape) was the Trifecta tune. The full tune includes selecta-tune, which essentially gives you a choice between stock and performance tunes (it's actually an Eco tune, not stock, but it's pretty close to stock)
I experienced no problems with the tune, other than the fact that the increased power led to an increased tendency to try and Use that power, and to getting more and better mods to leverage that power.
Under performance the power will be delivered a little more unevenly, since the stock tune deliberately dumbs down everything to a "lowest common denominator" so you have a consistent ride... that means anything that might give you more power, from cold air to spikes in the powerband, are choked back to that worst case scenario. Trifecta takes the gloves off, which almost always means more power, but a little less predictably.
For me, this is only noticeable at the high end, "wide open throttle", at lower throttle positions it just results in stepping more or less hard on the pedal to get the amount of power I want. Some people have complained though that they want something more steady.
The other thing the tune will do is let you benefit from other mods you do. While you will get Something from most mods on the stock tune, again it will be working against you, trying to dumb things down so your car drives like every other Sonic. So if you plan on doing anything to the car to get more power out of it, well, not only is the tune itself one of the biggest and easiest things you can get for that, it also is practically necessary to benefit from anything else.