Random Thoughts
10) Unfortunately rebase is problematic and can break an entire site. I've gone back and forth on simply removing the functionality. For now you just need to NOT have phpstorm running in the same directory you update from - i.e. update the site from one directory, then copy the updates over to phpstorm. Since you're a "developer" there's no plans to really change how this functions - you know what you're doing.
11) This would be cool I agree - this was the idea behind bundles. What you're proposing would be cool but would require a lot of work, so it's not likely to happen soon.
12) the marketplace query is a "heavy hitter" in that there are A LOT of listeners that do work on the listing - that's why it is currently set to what it is.