Any piggyback will always be at the mercy of the stock ECU. It can only trick it and alter it, and it is really hard to stabilize that relationship.
I believe tuning is the biggest limitation to the MSP, and a standalone is really the only way to get past it, but they have their own source of headaches. First of all, you need an accurate IAT to run a MAP based tune. So you'll need hard pipes so you can weld in an IAT bung close to the throttle. Lots of stuff like that adds up after a while.
I recommend running a parallel setup. Keep the ECU in to run the gauges, A/C, alternator, fans and to pass emissions. You can share all the sensors except the IAT, and then have your Halltech or AEM or Megasquirt control all fueling and spark. Use a patch harness, so you can quickly swap back and forth and you still have use of your car while you get things worked out.