E-manage I believe has more tuning options than the unichip
This is based on what I've read on the net and like everything on the net, should be verified by speaking to the ppl who will be tuning the car.

I'm pretty sure Speedworks and Xspeed (that I'm aware of) tune the emanage. Like all types of engine management tool, its as good as what the tuner can do.

With the filter, no idea what's good or bad. Most guys stick with the standard box with a drop in filter and still went well with it while others like the pods.