you have more options to program than stock ecu. In Greece where we have serious tuning and very good programmers no one from the serious i mean uses stock ecu. NO ONE. If you want pure power with much options you will use a new ecu or emanage like stuff. CHECK yourself and if you find a serious tuned car with stock ecu i will be glad.
About 6-7 years ago most tuners here shared the same view and e-manage was a very popular ecu. However, like many things, electronic advances are very quick and since software and systems have improved greatly over the last 5-10years people have started to stray towards either a standalone ecu or a modified stock one, especially when it comes to Nistune. This is perhaps something which has not been adopted so much in Greece and is more of a UK thing however.
While you believe e-manage is a better solution, having used e-manage, Nistune and standalone ecus I can confidently say the capabilities fall in that order.
e-manage is ok but it not good value for money any longer and does not offer the same things. You would also not be able to have any advances in supercharger control if it weren't for a modified stock ecu.
Nistune, in it's initial form was quite basic, however it is a very capable system now and has a huge support network and does not come with the compromises that e-manage coupled with a standard ecu does.
Standalone is much more free but is one of the most invasive and costly systems, as it often requires a lot of supporting systems, like crank triggers, wiring loom work, different sensors etc. These are often the systems which those 'serious' people opt for, very few will be using a piggyback system like e-manage for that here.
I personally would not recommend e-manage, however if this is what makes you feel happier and you have the support of more tuners being available then this is probably a better option for you. Choosing an ecu that no-one can map, no matter how capable it maybe, is quite useless
I hope, whatever you chose, you get what you want from the car, as that is probably more to the point here
P.S. You'll be happy to know that there are plenty of cars here in the UK running on Nistune modified ecus making a lot of power.