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So unless the MWLL Mgun fires hot plasma - I cannot figure out how this gun could possibly destroy the Atlas just by shooting for long enough at it's torso. The same could possibly apply to AC2/RAC2 because of their low caliber.
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Now... what for you may ask? The first and most important reason is to add bit more realism to the game.
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since your argument is entirely founded on that you want more realism i just have to add the following not even going into gameplay reasons for which several pop into my head too:
your statment may apply to the second worldware and handheld weapons for only a small part of all the weapons there were even back then. but there are actually a couple of rifle/armor examples even from back then where the rifle would have penetrated. and even today there are still several weapons that are used by infantry that can penetrate even the much more advanced armors of modern tanks. and it moreso doesnt really matter which weapon fires but a lot more on which ammo is used.
but since we are talking about vehicle mounted weapons and not infantry this should shed some light on the topic for you:
gun for a plane (!) even that was developed around 1972 (!) that can easily shred any armor to pieces. in a matter of split seconds:

here the plane its mounted on:

and heres a madcat model of mwll (mwll wiki reference):

as you can see. even the guns size is comparable.
and its just one example of many.
if you dont believe it just type the name in google.
EDIT: one of the many videos you see the gun firing and see what it hits:
http://www.youtube.com/watch?v=2_4O3dqsQck&feature=related and keep in mind this gun is mounted on a PLANE not a ground unit.
now you may say there always would have been advances in armor too. well as long as theres projectile weapons and armor against them theres always some research going on that allows the penetration of that armor too.
even more so if you really would want more "realism" it would even be worse than it is now because ap rounds wouldnt aim for taking of armor point after armor point but rather penetrating exactly at the point of impact and wreaking havoc in the vulnerable systems behind it in a matter of split seconds. seeing the projectile guns from today mguns should be made a lot more effective if you really would want more realism

and just so no one can state that mech mguns are only small calibre weapons totally different of vulcans or something like that a quote of the mwll forum that states "MG is a basic classification for a large number of similar weapons manufactured by every house of the Inner Sphere and every Clan. Including "Vulcan" rotary MG's and single barrel squad support weapons.".
readable here:
http://www.mechlivinglegends.net/forum/index.php/topic,6427.msg87050.html#msg87050