After completing several small projects with WCF, I'm quite happy with what it can do.
However, having spent a brief amount of time looking into the alternatives, I'm struggling to find exactly what benefits/drawbacks I would experience from using Java based web services such as AXIS2 or Metro?
Obviously open-source is perhaps one of them and also breaking away from Windows Server/IIS, but I can't see much more?
In comparing these two approaches specifically, I would evaluate your overall productivity between the two. Assuming you have an option of pursuing either/or, I've found the logistical work around with Metro and AXIS2 to be higher than WCF.
Given that both of these are essentially access points, whatever system complexity lies behind the scenes in terms of compatibility are key decision points. Even though we live in a world of unlimited interop possibilities, I tend to prefer stacks where consistency can yield productivity and performance gains.
As for open-source, while there is greater volume on the Java side than with .Net, I've also found that more of those projects are built to support functionality that's missing in the Java web service plaform (RESTlet, for example.)
Getting out of Windows/IIS is certainly an option with Java/Metro/AXIS2, whereas with WCF you're stuck with that as your front-end server. I've personally found both to be (too) configuration heavy, so neither have worked as an advantage for me in that respect. However, alternative hosts for the Java combination are certainly a possibility, so that may hold more value in certain situations.
All in all, both platforms (in the aggregate) will have scenarios where they're more advantageous than the other. Where those scenarios apply in your environment is what I find most relevant.