Rich is better for the engine, it keeps the engine cooler by throwing excessive fuel for combustion.

Saying that though imagine lighting a match stick and throw a bucket of petrol over it, will it ignite? ( for arguements sake lets say no ).

Too much petrol for the light to burn, this is what is happening in your engine on a much much much smaller scale but basically too much petrol for the sparks to burn optimum, the result is a lack of power from the engine and a higher fuel consumption.
Thats the only real drawback of running rich, lose power and uses more petrol and also you'll get that black sludge above your exhaust tip as unburnt fuel is pushed through the exhaust.

Bearing the above in mind, the leaner your car is running the more power its producing, however there is a high risk that you will lean out and melt a piston or two and basically cook the engine.

This is why cars from factory runs rich and never lean since they dont wanna have engine warranties issues from lack of fuel.

People who are into performance mods gets a piggy back controller like the Apexi SAFC II which controls also the air to the mixture for optimum power. Your tuner should have some experience and should be able to tune your piggyback computer for maximum power with a safety buffer not to lean out at any particular rev range.

The causes of cars running lean is usually to do with the air intake setup, if your car is stock then your air flow meter could be dying and needs replacing.

Say if you got a badly designed ram pod filter, when the car sucks air into the filter the air inside the filter could be travelling in all sorts of patters, from swirling to bouncing back and forth around the pod piping, usually its when the case of when air is travelling in a swirling manner. The problem is as it swirling like in a shape of a tornado it may go past your air flow meter without swiping the sensor, the ECU detects that theres no air or not enough air coming through the filter and it calculates with the amount of air is available to mix with the fuel, a small amount of air is to be mixed with a small amount of petrol and thus your car is running lean.

It is usually the pod filters that causes the car to run lean.

On the other hand when your car is running rich its due to the aftermarket exhaust, more free flowing exhaust means air can be expelled faster out of the engine and thus more fuel is used to keep up with this.

If you put the stock air box in then it should run normal again, if you have already got a stock box then get your sensors checked out cause it could be feeding your ECU the wrong readings.