To OP yes and no. I agree with the balance issue in that a chassis needs the same flavour but some mechs having particular quirks should stay. The Grid iron's gauss charge, the BJ-1DC's AC2 quirks, The CN9-D's LB10-X, The AWS-8Q PPC and DRG-1N all need to stay IMO.
Boosting these mechs in the IS gives them a reason to take them over another in the same chassis so there is always at least one strong performing variant. What most people seem to be overlooking is that a quirked build is usually a niche build as the mech is built around its primary quirked weapons for example the dragon. Take that enormous right arm off and it's goosed. Its a matter of advantage offsetting that's key here.
Remove the BJ-1DC's auto cannon quirk and it's now redundant there is now no reason to keep it as the same build can be done on other variants. Same goes for a lot of the Centurions hunchbacks etc etc. i'd hardly call them quirked meta builds as yes you can load up on a particular quirk but that doesn't mean that that mech will now be all powerful as everyone should know by now that you aim to destroy your enemies strengths first (i.e. dragon arm, Awesomes side torso's catapults ears).
Removing the mechs individual weapon quirks will render some mechs redundant immediately have little to no reason to take them over the next. This segregates mechs nicely removing any uniqueness means you have to find what you want with a different chassis.
Edited by mad kat, 17 September 2015 - 07:38 AM.