Only humanoid shaped ground units can operate in space as long as they have jump jets. The "Humanoid" requirement seems arbitrary and nonsensical, since vehicular jump jets are a thing, as are quad mechs.
The ruling that DropShips have K-F stuff in them enough to mess with a jump which is why the have to be attached to a collar. It was to prevent people from filling cargo bays full of DropShips bypassing collar limitations. It causes more problems than it fixes, and seems far more abuse-able that the problem it is meant to fix since now you can just interdict anything by docking a DropShip to it.
The Lack of diagrams explaining the different levels, elevations, and altitudes between the hard ground mechs are standing on and open space. A diagram that not only showed the different levels together, but showed their scale in relation to each other, and the interface point between them would be great.
Lack of terrain. Clouds should have some effect, storm patterns, etc. In space nebula, solar flares (they can effect things throughout a system, so I am not talking about right next to the sun), etc.
The utter lack of range diversity in capital scale weaponry. There are only a couple medium range capital weapons and no short range ones until you get to sub-capital. Every warship is a long range combatant, and that is kind of boring.
The limits on the total strength of a weapon bay coupled with bracketing fire making the strongest individual capital weapons suboptimal choices in every case. They are basically fluff pieces taken because they are scary, not because they are effective.
Fighters not paying in tonnage for their structure, unlike literally every other unit type in the game.
Docking collars being so fragile that expending thrust while anything is docked to them has a good chance of destroying them.
The arbitrary things that can't legally be put on a large aerospace unit, like MASH Units or Field Kitchens. I realize they automatically get the number needed for their crew, but it is illegal to put extra on, so you can't make hospital ships and such.
Screen Launchers being able to cover an entire space hex, but nothing else can? No one has made a warhead that shreds an entire space hex at capital missile range? Really? In fact capital weapon selection in general sucks.
Every aerospace unit capable of flying in the atmosphere and in space can land vertically, except aerodyne small craft. Why? They use almost identical construction rules as dropships, they function in almost the same way, excepting a few other minor things, why can't they land like everything else can? Makes no sense to me.
Ground Vehicles with large crew can ignore many multi-target penalties, but warships with hundreds of crew can't?!?! Seriously who thought that was a good idea? Every single capital weapon has it's own gunner, but they suffer penalties for targeting different things on different sides of the ship?
Sub-compact warships are DropShip sized, but can't be made to fly in an atmosphere. The only one we have in cannon is even shaped like DropShips. I've seen some of those DropShips if they can fly in an atmosphere, anything can.
The weight gap between subcompact and full warship. It bothers me.
Almost everything in the often vague and unclear satellite rules. The only part that is completely cut and dry is the design rules for them. Everything else is a mess.