I agree. The startup process could be more user friendly, but b91 is not difficult to figure out. You can just click the maptool.jar file and it will just run but because of some of the complex frameworks out there the defaults don't cover the memory constraints. So, you click on the launch.jar to configure it. Someone who is computer illiterate won't know what all the numbers mean or what ranges should be used but like you said there is plenty of support on the threads for someone to get those answers. I even made a video showing the full install process which takes about one minute for me to start from scratch and be in MapTool. The video goes on with how to add a shortcut to the windows taskbar which is a Windows thing.
I look forward to when MOTE comes out because it will bundle java with it, one of the main confusions with users and getting MapTool to start correctly. But they are only java 7 compatible and java 8 doesn't play nice when java 7 is installed and may be a hurdle for them to overcome.
MapTool is java 8 compatible but some changes in the libraries (I notice java 7 to 8 size is now 4x as big) has caused some unforeseen problems, but are mostly fringe cases. MapTool development is totally volunteer and a community effort so the bug fix cycle is unfortunately very slow. So, MapTool is what it is. If there is something you want to change the tools are out there for you to fix it. Otherwise, we'll have to rely on the good graces of others and have a little patience.
I'm also looking forward to MapTool 1.4 which is where much of the volunteer time is going. I know far less about it's development than MOTE because they're not on the clock to finish it like MOTE is. It'll be done when it's done. MapTool is a labor of love and so far, imo crushes all the other VTTs in functionality. I think of MapTool as the linux of VTTs. It's great because it'll do what you want but you have to be willing to put the time in to it to get results. Personally, I'm a Windows user for the ease of use, but if you want something bad enough you'll do the research to get things working the way you want.
If you're interested in a proper install you can go to MapTool - How To - HOWTO: Install B91 and set up Shortcut
* Please don't take any of this message as a slight against you. Your feeling is shared by many people and I'm just trying to present my own personal take on it.