The problems are endless.
A major trend I've noticed in elite is the emphasis on player hours (aka grinding). I can understand they are trying to make the grind a fun part of the game, but Grinding always favours players with vast amounts of free time. I would prefer ships to be much cheaper and less grind intensive, but have a more emphasis on running costs and damage management I would get rid of the 1 click repair all in the station menu and make keeping your ship in good condition part of the game-play. Also adding a second hand market for ships and parts to the game could be an important game-play aspect for keeping costs down.
A working example would be something like- you start the game in a sidewinder. the most popular ship in the game. This means that naturally, they are cheap as chips and every station in the game (including outposts) will have new and used parts. If you get a sidewinder shot up its no big deal. on the flip side, if you get your imperial clipper shot up, be prepared to feel the burn and spend your time collecting and having parts fitted to your ship (also downtime could be a factor in running multiple ships to compensate) This would come into its own at conflict zones where the heavy fighter class like the Vipers would be made to be repaired cheaply and quickly by any engineers (contract that with the imperial Clipper and expect to have to find a large imperial station to have parts fitted at imperial engineer prices)
Rather than the engineers update I would have just had an engineers tab added to the station for the above example, they would be charged with fitting parts you buy for upgrades and repairing your shot up ships.
The list is endless to be honest.