I do believe the Logic stock B3 does sound nice compared to many plugins; whoever engineered that one knew what they were doing to make it sound that good and be light on resources!
Everywhere I go, people really seem to dig the IK B3 - it's nice, authentic, sounds fairly comparable to what you will get out of a modern Hammond keyboard, ect. It was a bit overpriced on release, but they keep cutting the price; at $70 currently, the value is definitely there. It can be a little hard on the CPU but then so is my plugin (IMO, programming a realistic sounding Leslie/B3 SHOULD place demands on the CPU). GSi is still a good general purpose plugin, but IK is undercutting them at that price point. Most of the plugins out there still lag a bit when it comes to distortion - usually simple ATAN algorithms and such - so for that particular use case, I prefer my plugin and the vacuum tube simulations in there.
I also believe that there can be a slight difference between a beautiful sounding plugin played solo and something that sits nicely in a mix without a lot of effort. Not that you can't EQ or engineer one to fulfill the purpose of the other, but I think sometimes we get a little carried away with thick, beautiful, layered, detailed, wide plugins when, if you listen to many recordings, if the organ isn't the main event, then it's often sitting into the background or adding ambience. There are a lot of beautiful, detailed sounding plugins out there, but when I'm writing music, sometimes I just want something that sounds like a dirty old natural recording, and this is why I still give the Logic Organ props; to me, something like that can sound a bit more natural at times, and when I was making my plugin, that's more the kind of sound I was chasing, but to each their own.
As far as business practices go, not a big fan of most software companies these days. A long time ago I made the decision to steer-clear of DRM, subscription models, markdowns/sales and all that other nonsense; probably bad for business and my livelihood, but I think the world would be a nicer place if people charged a fair price for things and if you outright owned the things you pay for (like in the pre-internet days).
Perhaps have a look at my blog, or better yet, my B3 shootout video, where you can directly compare the sound of each organ - the Waterfall isn't in there as it wasn't released yet, but I will likely make a new video soon.
At the end of the day, these are all just different hammers that will hit the nail in slightly different ways...