I think that the best way to balance clan and inner sphere technologies would be along the lines of the direction PGI is currently heading, though with a few tweaks. Clan weapons NEED to be nerfed because they are inherently far too strong for an online game, but I think they should maintain roughly [10-20%] better damage/heat/range/tonnage and compensate for this by giving the Inner sphere mechs/pilots melee weaponry.
In cannon clanners did not use melee combat, and it makes sense if that were to continue. If clan weaponry maintained an advantage over inner sphere technology, then having clan mechs would change tactics from having inner sphere mechs, thereby promoting a more tactical playstyle and rewarding strategy. Knowing what you're up against would matter more (Looking at you information warfare!) and commanders who are able to strategize and out manuevre their opponets would be rewarded for their efforts (imagine sneaking up on a clan star with ECM and melee weapons, then crashing down on them at short range where you are able to circumvent their advantage, or forcing that inner sphere lance to come down the bottleneck where your sharpshooters are on overwatch
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Whereas if clan tech is turned into a purely flavor based choice with no mechanical benefit, (like if lasers deal more damage over a longer time, but effectively the same heat/second and/or heat/damage) then the game would be headed closer to a homogenized BORING gameplay that requires little to no tactics and doesn't reward pilots for building and playing specific roles.
I also believe that melee weapons should deal an extremely large portion of damage, lopping off an entire limb or dealing severe damage to a side torso, but this would be balanced by a [4] second animation of removing the weapon from the mech you just impaled/chopped during which time the attacker is unable to do anything and is vulnerable to counterattack from both the melee'd pilot and his allies.
Further along this idea we could use the melee dmg rules from tabletop, [Hatchet "dealing a point of damage for every five tons of weight." Sword "dealing a point of damage for every ten tons of the 'Mech's weight, plus an additional point."] This would force inner sphere pilots to further define their roles (and tonnage!) for what they want to do, being a melee specialist with a only 5 ton hatchet wouldn't make much sense, and using 5 tons on a weaponry based mech for a melee weapon wouldn't make sense either, further promoting role warfare and most importantly an extremely well balanced mechanic that allows people to specialize for what they want to do, be good at it, take their glory and honor in excelling at it, while not ruining the game or making anything overpowered.
Comments/ideas for how you think this should be done are liked and encouraged, lets discuss it and if we all like this then lets present it to PGI people ^.^