The new rules draw on my experience in the real-world arms trade, and try to simulate things like smart munitions, layered missile defences (Area, ECM, Point, Decoy,CIWS) and such.
The penetration/damage system means that there is a serious tradeoff to be made between weapons that can punch a hole in a big Mek's armour but cost a lot, and volume of fire.
Forex, the Free British Huscarl Mek mounts two pairs of twin 40mm cannon and a pair of HMGs. At close range, eg in urban terrain, it's ideal for chewing up lighter Meks fast, and it's awesome for getting rid of satchel-charge-armed heroes. It has real difficulty doing anything to a properly armoured Mek of simialr size though. It's cheap and, used right, effective. But a battlewagon it is not.
On the other hand, you could build a Mek of similar size armed with a hypervelocity cannon (the 'poor man's rail gun') which has awesome penetration but not particualrly great damage - and a high price tag. Such a Mek would be able to hurt big heavy units, though each hit would not be very serious. (Try fighting with an intact Mek whose fire control computer is Degraded due to a single penetrating hit and you'll get an interesting definition of 'not very serious'!).