In XI 3.1 SP3 WACS may have query builder (at least I heard it was going to be there). You have to have a java server installed no matter what (WACS or tomcat) You would make things much easier on yourself if you installed tomcat going toward the future (control panel, add/remove, BOE). There are no plans to port the CMC on .net and WACS is not as capable as tomcat yet. This would get you query builder and solve a number of future .net shortcomings you will likley run into going forward. While IIS /.net are supported I would consider that support in a very limited capacity as opposed to java/tomcat.
For CMS query and reporting, have a look towards CMS/Connect Community Edition from Infolytik. It's a completely free plug-and-play universe and driver that sits (live) on top of your XI3.x installation and fetches most of what Query Builder exposes and more.
The obvious upside is that you can run your queries up against your auditor DB and start to mix and match metadata analysis all from Web Intelligence. You don't need to install any server s/w / tomcat etc (although, as Tim pointed out - it's the better stack to deploy) .
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