Weak Top Armor
This quirk can only be applied to ground-based support vehicles. The point value of this quirk is equal to the BAR reduction from receiving high-angle attacks. High angle attacks are those from attackers whose total height advantage in levels matches or exceeds the distance to the target in hexes. For example, a BattleMech attacks a tracked support vehicle in an adjacent hex of the same level, in which the height difference is one level, and the distance is one hex. Units of equal height, such as conventional infantry, can also qualify if they are in a high enough building or hex level. While airborne units always qualify by default. This BAR reduction is not applied to AE damage.
Weak top armor would also be weak vs artillery, Mortars, indirect fire, and similar plunging attacks.
Center-line Weaponry
Mounted weaponry has a more restricted firing arc, having been reduced to a single line of hexes. Guided missiles are excepted from this quirk.
Can the unit use a Movement point to turn the hull to bring the weapon to bear? I.e. if the enemy is 5 hexes out but 2 hexes over, the mounting unit would spend 1 MP to turn the hull so it could fire the gun at the enemy unit that is off-center. This would be restricted to if the unit could make a turn at the end of its current movement. A fun idea is if the unit has to remain semi-stationary while rotating, so enemy units have an easier time shooting at it.
There are other missile launcher types. Damage per missile can also change with ammo types. The only consistent is that the bigger the launcher the bigger the potential damage.
The key is that if you base pts off tonnage, you provide an advantage to LRM-5 users. By making cost proportional to damage, people are less likely to cheese their designs to use lots of a single launcher.
Bigger launchers do more damage, but you can mount more than one small launcher for the same tonnage. I'll compare four LRM-5 vs LRM-20:
A single LRM-5 masses 2 tons
A single LRM-20 masses 10 tons
Four LRM-5 will mass 8 tons and as a result will cost 8 pts.
One LRM-20 will mass 10 tons and as a result will cost 10 pts.
On average four LRM-5 will do the same damage as a single LRM-20, but if you price it per tonnage then the LRM-5 user gets a 25% discount.
If there are other missile launcher types, then compare those missile launcher types while keeping as few variations as possible (i.e. regular LRM-10 vs Streak LRM-10).
If damage per missile changes per ammo type, then compare identical ammo types across different-sized launchers (i.e. Artemis LRM-5 vs Artemis LRM-15).
Otherwise you get the battle test for the Mackie that had new weapons and new armor only on the Battlemech, and the test result concluded that the humanoid form was what allowed the Mackie to win.