Based on my experience with Wix and InstallShield, I would recommend using InstallShield unless you need a fairly basic and straightforward installer. I say this because the huge Wix learning curve is made even more difficult by the lack of information available
There are no books on Wix, so your resources are limited to the Wix tutorial, which is detailed and lengthy but still doesn't cover much beyond basics, and blog posts you find via Google. Granted, there are many good blog posts which detail how to accomplish specific things, but unless you don't have deadlines to meet, you probably can't afford to sit and research how to do specific things in Wix for days at a time. Personally, I found myself doing this way too much for Wix to be a feasible solution (again, unless you only need a simple installer)
Ultimately, in my case, we had existing installers which were developed with InstallShield and we are simply able to be productive quicker with it. InstallShield also has its own scripting language which has pretty good documentation too.
Another big plus for me was that InstallShield eases the pain of multiple instances (try searching for how to do this with Wix and you'll get an idea of what I'm saying) and upgrading/patching. I was able to accomplish both of these (especially multiple instances) in a fraction of the time with InstallShield than what it took to accomplish in Wix.
My advice would be to choose based upon your time constraints/deadlines/commitments, complexity of your installer, and maturity of your product. Wix requires LOTS of research for things InstallShield provides a fairly quick way of doing. This can be even more painful if you have a mature product versus a fairly young product.
Hope this helps.
