Let me start off by telling you that I understand your frustration. Moving from one system to another is almost always a frustrating experience. And it seems that the more knowledge and experience one has in the first system, the tougher it is to see how all of that will be possible or easy in the new system. I have worked with both Minitab and JMP for many years. Both systems have their strengths and weaknesses.
I will also say, that as you move towards the level of understanding in JMP as you obvously have with Minitab I think you will find JMP has some features that Minitab just can not compete with.
But let me attempt to address some of your stated concerns.
Your statement about the ease of opening a project in Minitab, and then having it save automatically all of the data tables, analyses, graphs, etc. is very nice. And it works well with small to medium projects. In my opinion, the current JMP project structure works far better with large projects, with data from multiple sources. Minitab data tables, excel spreadsheets, raw data tables, webpages, etc can all be integrated into the project, and that project can be saved and passed to a collegue, and when opened, the complete file structure of all of those folder and files are available to them, in the same structure as the originator of the project.
More often than using a project, I use Save Session Settings. This is a great feature, that lets you save the entire envionment you are working in, to a single file. And then at a later point, go back and run that saved file, to recreate the total environment you were running in. I would check it out.....it is a nice feature. And, you can save as many of the different Session Settings as you want.
Concerning your statemet of saving each data file separatly, and each graph separatly, I think this is a point were the JMP pardyme is different than Minitab. JMP has a very strong scripting environment behind the scenes of all of JMP. And JMP uses it to make the system work to its advantage. You stated that you have been saving your graphs to JMP Reports, which require you to embed the data into the file. What I believe you should start looking into, is the saving of the graphs, into the JMP data tables. Well, actually the graph isn;t saved, the the script that will regenerate the graph is saved. And, you can save as many of them as you want into that data table. And it isn't just graphs, all of the platforms in JMP can save their scripts to the data table. And then brought up and redisplayed whenever you want them. Additionally, any Local Data Filters are saved with the scripts. Using this technique, multiple data tables are not opened up like they are if you save your graphs as JMP Reports.
One final comment. One of the major paradyme differences is the concept of interactivity. Minitab, for the most part, generates static output. Making changes to analyses and graphs, requrie that you go back, (CNTL/E) remember that key pattern, and rerun the graph, or analysis. JMP assumes, that you are exploring your data, and the filtering, setting, colors, etc should be done interactively, and that maybe from what you discover on the display, you need to take the identified data and move on to additional analyses. That capability is where JMP really shines.
I hope this provides you with some insight on helping you move more smoothly into the JMP world. If you have more questions, don't hesitate to post them in the Discussion Forum.
Jim