Again, I'll suggest it here. Everyone play the game just taking the Primes and see how it feels. That is Battle Tech. That is what feels right.
I'm pretty skeptical that the stock weapon configs for a board game would directly translate into a PC simulator any better than the myriad of other assets the devs already have to rebalance. Not saying it's impossible, but it seems like it'd happen less than half the time. The combination of widely different weapons that seems natural for a dice system doesn't always feel right when you actually have to aim a cross hair and press a limited number of mouse keys.
There must be some sort of middle ground between the fruit salad approach to weapons loadout of BT board game and pure boating. I don't want to be forced to have all 3 weapons type (energy, ballistic, missile) on most mechs I pilot simply because that's how BT rolled (literally), but that doesn't mean I'll las boat every mech if I'm given mechlab.
As for customization in general, my opinion is that people will tend towards fewer variety of weapons on a mech because that's how it works in real life. You don't want to juggle several widely different systems with different ranges, ballistics, locking, travel time, etc.
Most combat vehicles today have only an average of 2 weapon systems per gunner (who doesn't have to drive the vehicle as well), the major exception being aircraft. Given that mech pilots have to drive and gun, plus manage comm and sensor, it's not surprising that many would move towards less loadout variety (I personally stick to only guns and lasers of similar max range whenever possible), rather than BT's insistance on putting guns, lasers AND missiles with all sorts of ranges on every other mech.