They're two completely different animals. The stock ECU will be easier to get smooth drivability, idle, etc. However that's not to say at all that MS3 will be able to be smooth, it will just take more tuning. The main difference is whether or not the features are worth the extra cost to you. 2-step launch control, timing retard after launch, traction control, flat foot shift, several generic sensor inputs, auto-tune, flex fuel and table switch, SD card datalogging, nitrous control, water injection control. The features are enough to make me use MS3, I'll be using MS3+MS3x in my Miata swap (I'm currently using the MS3 on the 4 cylinder).
I have a Racepak iq3s as my dash, and an 8" tablet mounted in my radio delete for tuning and more data. My roommate is using his tablet as his main instrument cluster. Tunerstudio works great on a tablet, and makes tuning on the fly very easy.