There arn't really any pro's and con's.
Both the APR and the Milltek are as good as eachother - in terms of quality, fitment, performance gains etc.
You need to take into consideration the following:
Price (the APR is slightly more expensive)
Noise (both exhausts sound completely different to eachother)
Tailpipe design (again, both are completely different to eachother)
You would benefit hugely from seeing/hearing/driving both exhausts in real life, and then making your final decision.
Hope that helps.
