In SC2, when we obtained technology to make a lander better, better shuttle craft lander were made.   If we started the game with the equivalent of a Ford Model T lander we finished with something like a Rolls Royce or a Lamborghini.  You couldn't lose an improvement because the base lander became better.

In SCO, the approach is different, modules kept on the main ship make a Ford Model T lander behave more like a Tesla.  I suppose that the modules are kept on the main ship because otherwise, when your lander is destroyed, the improvements aren't lost.   The idea here is to be able to customize your lander for a specific mission to a planet.   

The problem with the SCO approach is that the only way you can customize your lander is at a starbase.   It is just not practical.  Imagine if Captain Kirk or Picard on Star Trek had to go to find a Starbase in Federation space every time they wanted to send a customized shuttle craft on a mission.  It's just not practical.   The only way the SCO approach would work to customize landers is if we can do it when we are in orbit around the planet.   The lander specific slots could be customized, this way, if we need extra armour or extra corrosion protection for a specific planet in the system, it would be handled in orbit.  I also don't get why we would still want to build a Ford model T lander once we have better armor tech or better engines.   Why use up a slot for better engines, when you can build your next lander with a better engine ? Imagine we know how to make a chainsaw, but instead of building a chainsaw, we still build a handsaw but use some external module to make the handsaw perform like a chainsaw from a distance.  It's just a weird complicated way of looking at it.

Another possibility would be to find more advanced lander types abord those wrecked ships that litter the various planets.

One other thing that annoys me about the current system:  We have a lander capable of blasting off into space from the planet, but whose same thrusters are unable to climb a steep hill.  This makes no sense.  If you can blast off into orbit, you should be able to climb up any hill on the planet.   The Ruby world are particularly annoying for this.   This makes the ressource gathering more tedious than it needs to be.