One could say that you are also contributing to part of the problem with the game. You are stuffing small stuff into vital areas to fill out crit slots, not because you need a small energy weapon in the head, but you are trying to work the system to reduce the chance that a critical hit to the head will have less of a chance of hitting your pilot. The core of the problem here is that you are treating the game as a game and filling out your designs accordingly.
The question is if this is any different from using nothing but pulse lasers and targeting computers? In a realistic sense, targeting computers and pulse lasers should be rather dominant in most designs. We can throw out the "but targeting computers are expensive/rare/ hard to produce/only X faction has them" since people seem to think that a universe where "Life is cheap, Battlemechs are expensive" suggests that all combat would be conducted using battlemechs instead of rarely. If you see a single mech you should see a company or half of one of vehicles, and at likely 2 or 3 times as many infantry since there are a few types that can easily keep up with an assault mech. Lets not even get started on how often assaults should be seen versus how often they are seen in game!
If the games are being balanced by BV2 then you really shouldn't have a problem with the pulse+TC combo as they are paying for that gear. It might be annoying in game when you can't hit the side of a barn, or even a mountain painted as one. That is likely the issue, not that the pulseboat is invincible. What you should look into is inferno SRMs, plasma cannons, and battle armor with flame throwers. Start roasting their mechs and see how effective they are at sinking additional heat. The good thing about the game is that there is always a counter to something.
Regarding the question, the only time that I really used many customs was when I first got into the game and all that we had were 6 or so designs in the back of the rules book at the time. It was a necessity, but beyond that point in time I have used mostly stock designs. There have been a few modifications, but that is mostly removing a medium laser for a ton of armor, or C3 that someone else used. I don't really count ammunition as a modification, however if one does then that is the vast majority of my mods.
Some of the stock designs have issues, but then again what machine is perfect? The stocks are designed in a way that a company would design one, not how a player in a game would. Some of the compromises are still odd, and I hate the Atlas K variants for their single heatsinks. That is one of those variants that I might use, but might consider modding, but likely mod and then scrap it.
Of the mods in the past 5 years, I have tried to post them on a forum ahead of time so that nobody is surprised if it shows up on the table and needs an excessive amount of time to go over it. It assumes that the players are even familiar with the stock design in the first place, but I would rather it be known since I have been playing more in teaching mode then to win.