With the docking system it is next to impossible to dock if you have a really big ship (like really big, and I can't live without my star destroyers :D). Also, it is just hard and annoying. My ship constantly goes through the floor when I am docking and then I have to dig it out of the ground with the build tool, and with some of my bigger ships it is probably going to take a thousand docking enhancers. What I suggest is make docking enhancers more effective and possibly make a area around a factions homeworld in which ships are automatically considered docked. You could possibly make a VERY expensive node for this if this seems too overpowered, and possibly nodes (very expensive) that add area to the faction base. Also, if you wanted to keep regular docking, maybe add different tiers of docking enhancers that add more space, but you only have to buy 5 or 10 instead of 250 or 400. It probably wouldn't be worth it to take the time to destroy my BC-304 Daedalus, but I don't really like all the holes in the hull :/
