The System i Network references a Forrester report on one of its stories looking at the integration of Windows and System i. Though doing so might be a good idea, helping to both modernize your IBM System i and tame your Windows server jungle, there will doubtless be some hiccups.
There is effort involved, both in integration activities and the initial work. On the other hand, the benefits often make the effort worthwhile.
IBM is especially keen on promoting BladeCenter connections to System i.