Everything has a downside:
-Tuning a car any more than bolt ons will have tons of issues. See:
http://www.honda-tech.com/zerothread?id=683477
-Intake and exaust make the car better in the upper end and less in the low end. If they don't then they make the car too loud for normal people.
-CAIs are too loud and odd sounding for normal people, like your grandparents. It's a luxury car right? It's also a liability to them if you suck up water and destroy your engine.
-Dropping makes the ride worse, no matter how good your suspention. You can have an adjustable roll center and fully controlable suspention components but the springs and dampners have to be stiff to keep a lower car off the ground.
-Only a few people like body kits and Altezza lights, and even less have your favorite as their favorite.
-Lightened flywheels make your car harder to drive. It has less inertia so the clutch control has to be near perfect.
-Stronger clutches require more control as well.
-Sway bars(roll bars) make the ride jarring over uneaven left to right surfaces.
-Strut tower bars make the car too twitchy for many people, and can cause the car to loose it's safer understeer balance.
-Big rims make the car twitchy at the limits, reduce snow traction, and wet traction. The
overall car gets worse.
-Big rims also raise the unsprung weight, making the car uncomfortable.
-Wide tires reduce gas mileage and stability in low traction conditions.
-Gimmick spark plugs (Splitfire, Bosch Platinum4+, etc.) only last longer at the stock power. Replacing worn spark plugs raise power anyway.
-Hyper-Ground and MSD are cost prohibitive, and may not really raise the hp b/c you replace the above when you install it.
-NOS kills your engine like steroids and is horrible for the environment. The remaining NOx destroys your cat. I've heard that they don't mess up your cat and I can prove to you with logic it's a lie: Your putting more Nitrogen and Oxygen in the chamber so you can burn more fuel. There WILL be extra NOx from ambient Nitrogen combining with the oxygen instead of carbon combining. In any case, more fuel burned means more bad gasses, period.
-Turbos require a lot of engineering knowledge, destroy the engine the same as NOS, and are very cost prohibitive to the manufacturer. The same T3 has been used in almost every factory turbo, with only slight modifications.
-Blocking the reduces emissions considerably and the manufacturer would be fined for this.
-Neon breaks very easily.
-Alarms, shaved locks, shaved doors, etc. are really useless and make getting in a car with a full load of groceries that much harder.
-Stripped interiors are just ugly.
-Carbon fiber is very, VERY cost prohibitive.
-In Dash receivers are cost prohibitive, the manufacturer can make much more money by making their own stereo.
-Subs use power and all the controlls to keep the power up are cost prohibitive and bulky.
-Everything that gives you performance reduces gas mileage and/or costs a lot and/or is hard to maintain.
-Everything, and I mean EVERYTHING, has a downside. Just ask me and I'll probably have a downside to it (not to be all pessimistic and all).
There is a reason for the factory not putting on that nice looking strut tower bar for you! If it was an overall good idea then they would have it on all their vehicles. They don't want to make a slow car. They want to make it an efficient car, comfortable car, reasonably priced car, easy-to-drive car, etc.
EDIT:
OH yea!! I forgot!!
-Big brake kits are cost prohibitive and usually too big for the factory wheel size.
-Drilled and/or slotted rotors can break when in cold, wet climates.
-Steel brake lines are cost prohibitive.
and LBNL:
-Racing pads are a nightmare b/c they have to be at a proper operating temperature to work well. When cold they are MUCH worse than stock.
I'm not saying don't do it, by all means. I am happily modding my car, and I hope the rest of you are too. This is just so you know what your getting yourself into... Newtonian Physics aply to tuners just as much as Murphey's Law.