It's been no secret that I've favored InstallShield over WiX for many years. I've used InstallShield products since 1997 and I've shipped hundreds of installers using this versatile tool. InstallScript, XML Locator, Setup Prerequisites, Multiple Instance Support, COM Extraction, MySQL, Dialog/Control editors, Product/Release configurations and Component authoring wizards/views have made me a very productive and profitable person over the years.
Unfortunatly, there are also things I dislike about InstallShield. The DRM activation ( and now reactivation with IS2010 ) is horrible, difficulty in trying to get updates in an offline scenario (which we always are for security purposes), the random crashes, the horrible DTD/XML transformation, sequenced primary keys and of course, the removal of the stand alone build from Professional and totally useless collaboration tool combined with the really high price of the product.
If I'm hurting anyones feelings, I'm sorry. It's hard for me too since I've used this tool for so long and I do believe it's still a very good tool for many development shops. Just not for mine.
At my day job, I lead a team of 4 ( going on 6! ) setup developers. We collectively maintain dozens of installs that generate and consume hundreds of merge modules from a software product line. Our typical installer ships 10,000 - 15,000 files and includes countless databases, services, webservices and many chained packages of programs that we integrate with. All of this occurs on many active branches.
Unfortunatly InstallShield with it's DTD XML and incremented primary keys just doesn't work well in this environment. Merging branches back together in clearcase is a nightmare since you always end up with unresolved conflicts. Enter WiX. The XSD XML is 95% smaller then DTD XML and is way more expressive. Also thanks to deterministically unique primary keys and guids, changes done on multiple branches can actually merge back together easily.
The problem with WiX of course is the lack of gui designer abstractions and visualizations. Fortunatly I finally have a solution for that. I've recently had an internal tools developer assigned to me to come up with our own collaboration tools to sit on top of votive. Once complete we are hoping to once again try decentralized setup development. I'm not sure it'll work ( it didn't last time ) but we are going to give it a try again. The reality is our environment is growing so fast that we need to retool and try new strategies to keep up. Hiring more and more people just doesn't seem to work anymore.