Well I'm no great expert on this, but it's a cost-benefit thing really. By the time you've bought all the bits you need for an AEM it'll probably cost what, £1400 or so? Plus it's gonna cost you more in mapping time. Whereas an Emanage setup would be more like £400. The AEM is more flexible and can do extra stuff, but is it worth the extra? In either case you'd probably want a boost controller, if you go the Emanage route you might as well make it the Profec E01 and that would allow you to fiddle with the Emanage in the car and view stuff in real-time.
Here's some advantages and disadvantages for a starter, I'm sure someone with some more knowledge of stand-alones can add to these:
Stand-alone
Advantages
Complete control over maps means you know exactly what it is going to do at any point.
More flexible. You can get it to do stuff like anti-lag and change maps depending on the state of various sensors.
It plugs straight in (I think) so you don't have to wire it into the loom.
Disadvantages
Significantly more expensive.
You have to set up your maps from scratch, which is going to take much longer (and hence be more expensive).
Emanage
Advantages
Quite a bit cheaper.
Uses the ECU base maps, so you don't have to worry about cold-start and idle maps etc. That means less mapping time.
If you have the Profec E01 you can use it to display and monitor things in real time.
Disadvantages
Bit of a pain to wire in (not so bad using a Fields harness)
You know what modification you are making to the base map, but you don't always know exactly what the ECU base map is doing. E.g. with ignition timing you can modify the standard timing, but you can't see what the actual value is, just your modification to it.