I'm still not understanding why you think shares would be easier to set up. As I said before, you could easily use the CLI in the jail to use shares right now. The real killer would be the performance penalty of going that route. Setup really shouldn't factor into designing a server as you should only need to set it up once. On the other hand the performance matters ALOT more since it will be your limiting factor for as long as you own the server. In short, a little inconvenience during setup <<< performance of your server. This is one of the reasons why FreeBSD does most of its work from the CLI and not some prettied up user interface like Windows. Big picture though, I don't really see how shares would ever be better than the current mountpoints. Mountpoints are pretty straightforward. You chose the folder you want to pass to the jail and where to put it in the jail. FreeNAS really isn't designed for the most novice of users. Its designed to allow some of the more novice users get into and enjoy some of the performance and reliability benefits of FreeBSD without having to spend 2 years learning how to use FreeBSD from the command line.
As for the single user mode, I'm still a little confused as to what you are asking for. The whole purpose for single user mode is to allow you to troubleshoot/repair a server that is having issues. The times that you'd need to be in single user mode are typically when you(the admin) has screwed up and either made a mistake in software causing the system to be unusable or the server encountered a condition you didn't plan sufficiently for(for instance, a loss of power with no UPS). There's a couple of other situations, but you aren't likely to encounter those typically.
Many of the more powerful OSes don't make the decision to run a file system check(like what windows does on bootup sometimes) but leaves you, the admin, to make the decision with how to proceed. If the system is encountering a hardware failure causing reboots and then auto-triggering a file system check you don't want a server to continually reboot, auto-run a file system check, then come back online before a rinse and repeat all weekend. You'd certainly have a useless server by the end of the weekend. You'd instead want the server to keep itself offline and let you make the appropriate choice as to what to do and when. You'll find that many aspects of FreeBSD are designed to not be automatic when they could have been because the thought process is that the administrator should be the one making big choices and not some algorithm that might inappropriately think something needs to be fixed that isn't actually broken. In all honesty, I consider it very bad taste for Windows to automatically run a chkdsk when it thinks there is a problem. What happens if you have corrupted files? What do you do now since its "corrected" the deficiency without your option to not do the repair? And what files were corrupted? FreeBSD simply decides to make you monitor anything and everything that could be potentially devastating to your data. I think that the single user mode thing is something where you're going to have to swallow the bullet and accept it for what it is. The thought process isn't likely to change anytime soon, if ever.
I've done some really nasty things to FreeNAS in a VM and on real hardware, and I haven't had to go to single user mode yet. Mostly, I'm assuming that's because FreeNAS keeps the boot drive in read-only mode most of the time.