Hi, just saw this plugin (suprised I didn't see it earlier or was it only just accepted?) and I've started on a similar concept myself.  Just chucking some of my ideas out there in case you're interested - could be good so see them in a single plugin.  Running on a primarily PvP server so don't want to utilise spawning of minis but wanting to create an upgrade progress that would be balanced for PvP.

+ Upgrading requires the player to be parked near a T2 workbench (so you can't just upgrade in the wilderness, need to be at base).
+ Upgrading is initiated in game by hitting the mini with a torch (I think I tried electrical wire but it didn't trigger a hook) - this would bring up a gui to select upgrades to add/remove.
+ Upgrading can add searchlight, turret, extra seating, xmas lights along bottom of mini, tail light, storage (stashes or boxes), licence plate (with some obvious inspiration from other plugins).
+ Cost would include the appropriate item along with some scrap for "welding" the item to the mini.
+ Speed upgrades (if I could find a balanced cost, perhaps also require additional fuel usage), extra durability (costing scrap/hqm) or more fuel efficient by stripping off armour (leaving it at a lower durability).  Possibly mini trails so you can easily see that the mini is upgraded (others more likely to try and steal it).
+ I was also looking to see if I could make the turrets into permentant peacekeeper mode as normal turrets can be a bit OP (can also help in a PvE area).

I do also have a PvE dome in which players are able to spawn a "practice mini" with unlimited fuel.  Zonemanager is set to no fall damage in the zone, and TruePvE prevents any damage to the mini so players can crash to their hearts content.  The mini is instantly destroyed if players try to fly it out of the zone.  Perhaps a config item here for restricting the mini spawning to inside a certain zone - or even outside of a zone?  Or a separate command (e.g. /zonemini)?

The plugin was accepted about a year ago after I was notified that the plugin was rejected.  I did make a fix to the issue, but was told that it will probably not be accepted due to repetition.  I walked away from Umod and Rust a few weeks later due to being burned out.  The plugin went inactive a few months later due to my absence.  I just recently got back into Rust and writing plugins.

As far as your idea, that would a good learning curve.  I have thought of learning how to write GUI code into the plugin to make upgrading much easier and incorporating the cost into as well.  The primary purpose of the plugin was for the PVE players on the server I play on to be able to have a non-stealable minicopter that can be teleported to them. 

In addition to what you suggested, I have had the idea that if I get the GUI working to add in a hacking system that would allow players to be able to take ownership of the minicopter in x amount of time. Probably have the hacking computer spawn on it and lock the minicopter from use. In addtion, this would broadcast a message to authorized pilots of the minicopter (most likely team) so they know their minicopter is in the process of being stolen.

I know I need to add code to make this plugin more applicable to PVP while still having it be applicable to PVE with permissions and config file settings.  

Alot of learning curve to implement everything you have listed, but I will give it a go.