Firstly, you need to look at what makes the Blood Asp and Fafnir so good. Is it pod space, armor, speed, pod types?
The Blood Asp, weighing in at 90 tons, should have equivalent pod space, armor, speed, and pod types to the Madcat MKII, which also weighs in at 90 tons. Perhaps the MKII is slightly undergunned since it has been around since 0.1 and might have been built with fudged build rules unlike the more recent Blood Asp. Perhaps it is simply given a "better" mix of weapons because the devs loved it that much more and have had all the more time to play MWLL and figure out what weapon combos = death incarnate.
The Fafnir, weighing in at 100 tons, should have equivalent pod space, armor, speed, and pod types to the Atlas, which also weighs in at 100 tons. It has 2 siege slots, 2 assault, and 2 mediums while the atlas has 1 siege, 2 assault, 2 mediums and 2 missile slots. The Atlas has already been stated to carry a standard engine instead of an XL engine, so that goes a long way toward why the Atlas feels so much more undergunned than his Fafnir cousin, he's carrying ~20% less pod space.
So for the clans, I don't see the Blood Asp as being better than the MKII other than the weapon configs it has were just given more recent and more loving attention by the devs. The Fafnir, on the other hand, simply outguns the Atlas because it has more pod space and better pods. The Atlas being forced to use LRMs instead of mounting another LB20X or a Gauss Rifle means that it has a harder time concentrating damage with one big smack, where as the Fafnir is designed to do just that.
At the end of the day, it comes down to what the asset is designed to do. The Fafnir is designed to plod toward the enemy and punish anything that gives it more than one shot at it with the dual HGauss, while the Atlas is sort of designed to plod with the rest of his lance, provide AECM, LAMS, some LRM support, and punish anything that gets close with his LB20X. If the Atlas Prime had an XL engine those LRM-5s could be upgraded to LRM-10s, the PPCs to ERPPCs, some extra heat sinks thrown on it to keep it cool, the medium pulse replaced with ERMBLs, and the LB20X replaced by a Gauss Rifle. Then its role as a lance command mech would be much more obvious while leaving the close range rushing to the Fafnir or other Atlas variants.
I remember back in 0.1 the Atlas Prime had a load out very similar to the above, which also happens to be close to the canon 3050 Prime version (ERLBL instead of ERPPCs) but for whatever reason it was replaced with the LB20X version.
The sad truth is, as much as I like the mixed role mechs, the majority of players don't. They want something that can fire all its weapons out to the same distance, with the same travel time, and the same recycle time, with no ammunition or heat concerns, and that's pretty much what the new assault mechs are really good at doing.