Here's a list of things that really drive me up the wall with SR4.
#1: Diving and decompression.
If you've ever seen divers apparently being paid vast sums of money to just sit around and read the newspaper, there's a pretty good reason for it. Decompression sickness - or "the bends" - is caused by a simple law of physics: the amount of gas you can dissolve in a liquid is a function of how much pressure it's under. When divers go deep under the sea, the pressure is high enough that huge amounts of nitrogen are dumped into the bloodstream, which will go out of solution and bubble out exactly like fizz in a can of cola if you decompress too quickly. If you ascend slowly and gradually depressurize, you can minimize the risk, but you still need to wait around quite a while for the nitrogen to boil away from your bloodstream.
The listed effects of decompression sickness are "one box of physical damage per hour until placed in a pressure tank." It's much worse than that - ascending from 200 meters in 30 minutes will make you exceedingly dead. Also, if you get on an airplane the day after your dive, you get the bends anyway - there's still a lot of nitrogen slowly boiling away from your bloodstream, and it boils away much, much faster under the reduced pressure.
#2: Car modification
This one really puts a bee in my bonnet, if you excuse the incredibly horrible pun. I've seen modifications that violate about half the rules set in Arsenal done by men in sheds. A good example might be the swap between a 1961 3.5 liter Oldsmobile V8 and a 27 liter 1,600HP Rolls-Royce Merlin engine in an old Rover.
I'm not a mechanic, but some of this stuff doesn't even make sense under high-school-level physics:
1. Engine acceleration and top speed upgrades are ridiculous. There's only one thing which an engine produces, and that's brake horsepower. Top speed is a function of mechanical and aerodynamic drag (which varies with speed) and horsepower: when the energy consumed by drag at a given speed is equal to the peak engine output, you've reached your top speed. While it's possible to trade peak output for a little acceleration by tuning your engine for less torque at high RPMs and more at low RPMs, electronic valve systems being developed today would negate the need for a trade-off and a continually various transmission - which allows an engine to sit at peak RPMs while accelerating - means that it would be pointless.
2. Turbochargers, once spun up by exhaust gas, increase engine output by forcing more fuel and air into the engine, allowing for ten liters of fuel and air in a dinky two-liter engine. While efficiency is lost, this does make it to add a lot more power to a small engine in a small car - for example, a heavily boosted motorcycle engine can produce 500 horsepower despite being the size of a breadbox. They engage whenever the engine is working hard (and producing lots of the exhaust gases that power them), and can be seen working throughout fifty-mile courses on pretty much every rally car for the last twenty years.
What Arsenal lists is an overboost. A turbocharger's design means it's as simple as turning a knob to adjust the pressure at which air is forced into the engine, resulting in a bigger bang. However, doing this will overwork the turbo and put more strain on the engine, potentially causing damage.
There are additional flaws to turbochargers. Unless multiple small turbos or (ideally) a complicated sequential turbo system with multiple turbochargers of increasing size is used, a turbocharger can take time to spin up and begin delivering boost. One solution to this problem is an "anti-lag" system, which wastes large amounts of fuel for the sole purpose of keeping the turbo spun up and ready to supply boost. Another solution is to use a supercharger, a less efficient system powered by the driveshaft that has no spin-up lag at all.
3. Engine swaps.
With a little custom fabbing and some spare parts, it's possible to do some pretty weird modifications to cars - for example, I'm told it's quite popular to take the lightened small-block Chevy V8 from a crashed Corvette and put it under the hood of a mid-90's RX7, a car originally famous for it's piston-free Wankel rotary engine. I've seen V12-powered pickup trucks, and a Geo Metro race car powered by a souped up motorcycle engine, and Porsches with Subaru powerplants.
While keeping the aesthetics the same can be hard and not spoiling the handling can be harder, this is a good way for a mechanic with more skill than money to turn a beater into a speed demon.
4. Weight reductions
I may have missed this, but weight reduction is the #1 upgrade to any car ever. Reducing weight improves acceleration, sharpens handling, decreases body roll, and improves fuel economy. Quite a lot of weight in a modern car is from components not related to the mechanical or structural integrity of the vehicle; by ditching the heater, air conditioner, rear seats, thermal insulation, acoustic insulation, nav system, stereo, cupholders, interior body panels, and other unimportant items it's possible to do some pretty impressive things to a generic econobox.
5. Aerodynamic mods
By combining a variety of relatively subtle components - front and rear splitters, a small spoilers, some streamlined fenders - it's possible to make a big difference in performance. By trading downforce for drag, it's possible to vastly improve handling at the expense of top speed There's a reason why Formula One cars need 1,000 horsepower despite weighing about as much as my shoes - all the wings and spoilers that give it the tremendous downforce required to take a corner at 150MPH also result in huge air resistance.