If you don't wanna play with the class system, I've added a turn on/off function in the outsourcedconfig.ini file. I'll do this for anything new I add that might be in conflict with realism.
I know that there are many people that dislikes anything that isn't based on realism, but most of the criticism I've gotten is from people that has never actually tried it, only read about the changes on a forum. A long time ago I made some changes on grenade damage and got a lot of flak for it, but once people had actually played a little with the new setting the criticism ceased. The lesson here is, never complain about something without having at least given it a shot

(this isn't aimed at you Chortles, you just left the door open for me to get this off my chest

)
When talking about the 3 levels of player guards, I was mostly meaning their attributes. But I will give them different gear, the recruits will have cheap stuff while the elites will have the expensive imported stuff.
The economy will be a big task to delve into, and I agree with you regarding JA2, I tend to do the same as you there. Luckily there are a lot of factors that will be part of it, and with a lot of work we might get it to work. There is of course always possible to trick any system, and since there's an "Easy Money" option in the game, one could easily bypass any system we make.
I had an idea last night before I fell asleep, that always happens to me.
As you might know, if one hires a merc you can tell him to wait for you, and if that place is a "Standard" sector he'll wait until his contract ends. It might be possible to add some dialog options to a waiting merc, like train militia. So if the player wants to train the existing militia, he'll have to recruit a merc for it and leave him in that town. We could then play with the merc salaries to tweak the economic system. I think this will be worth investigating.