Okay, I finally have the time to reply properly.
The reason why we seem to continually butt heads over this sort of stuff is cause I spent over 7 years providing the lion's share of the SCP support before people like jr2, Jeff Vader and The E came along. I've seen just how badly people can **** up their installs and I've seen just how much of an issue people can have trying to move to a new SCP system (for instance it took years before everyone got the hang of the current -mod system and even now people still **** up occasionally).
Moving to this system would be a support nightmare because we'd have to upgrade every single installed version of FS2_Open to start using it. It's all very well to say that a combined installer/launcher would solve those problems but a combined installer/launcher would largely remove the problem causing the issue anyway (people who aren't familiar trying to install something). We could easily add a troubleshooting section to the launcher that flags any files that shouldn't be in the path and asks whether the user installed it himself.
If the -mod system had been designed this way in the first place then maybe things would be better but changing it now is not a good idea. The only way I can explain the monumental problems this issue would cause is to talk you though what would happen if you tried it.
So let's say you coded the changes and added them to an antipodes build.
Firstly you'd get comments from the people who usually hang out on #scp with you. They all know what you're up to and would be prepared for the change. They'd have no issues.
Then having made sure the code works you'd add it to trunk. You'd probably post an announcement saying that you've made this change on the SCP forum. This where problems begin. You're going to start getting posts from people who missed your post but who downloaded a nightly build and found that it doesn't work properly for them. At this stage it's all from developers and early adopters though so simply pointing them at the thread is going to solve about 90% of their problems. We're still going to have to hand-hold a few of them through making a new mod.ini though but that shouldn't be too bad.
That said we're going to have to deal with a constant trickle of threads like this for months (my guess, one or two a week until a major release).
Now let's say 3.6.11 is close to ready. We start pushing out release candidates. RCs tend to cause people to come out of the woodwork and test. They never bothered keeping up to date with nightly builds (and I can't fully blame them, it is a pain in the arse!) but they want to make sure everything will work with official build. This is already an annoying issue for the SCP but now we'd added the fact that most of these people will have missed the announcements and will be posting asking why their mod has suddenly stopped working.
And then we release 3.6.11. Now the major support nightmare starts. In a single stroke we've made every single FS2_Open install invalid. We have hundreds of different configurations for FS2_Open installs and none of them will work properly now. We're now expecting every single SCP user to find and replace the mod.ini for their installed campaigns. Not just the ones supported by the new launcher, all of them. Including any they are making themselves.
And that's just if we're talking about doing this manually. If we do this at the same time as the new installer/launcher comes out the problem actually gets worse because users won't know if the issue is due to the launcher or FS2_Open.
Then we get to the issue of the developers. Basically we're forcing a new system on them. Every campaign, new or old is going to be forced to update their installers to fix their old mod.ini files, and to changes their development installs to reflect the new requirements.
We've added yet another chore to the task of preparing a mod for distribution (and one that will often go wrong, for instance devs who can't use MV_Advanced will forget to include it in their released mod.ini files).
We've forced those users who do know what they are doing and have compiled their own favourite effects into a VP to manually change the mod.ini files for mods they download.
We've forced FSUP to never change the names of any of their VP files because it simply isn't worth the hassle of making everyone update their mod.ini files.
And what have we gained in the end?
-A system that is less intuitive that the original one. For all it's faults the current system is simple. Name a -mod folder and everything in that folder is used.
-A system that makes mod.ini files a requirement for the engine itself to work properly with mods (when previously they've only been an optional addition for the launcher)
-A system that doesn't really solve the biggest issue when it comes to people having ****ed up installs anyway, people installing dodgy files in the FS2 root directory.
If you had suggested this once the installer/launcher had been out a couple of years I'd probably still be against it. It's too much work for the support and development teams for too little gain. But suggesting it as something we should do now is crazy for the reasons I mentioned above.