When I got the car the controls for the a/c didn't work, power outlet didn't work, and front end made a clunking noise, but were fixed rather fast and covered by the warranty.
The brake rotors keep warping and have had to replace the pads and are in need of it again (just 5 months later).
The theft system acts up making you wait ten minutes for it to reset.
Some times the car has trouble starting.
The intake gasket has gone bad twice.
The alternator has went out once causing the battery to fail.
The water pump has failed, filling the oil with coolant.
The car has a bad rocking when at stop signs.
The glove box door is loose and rattles.
Check engine light comes on when it wants, and the shop can never find the problem. This caused me to take it to the shop because it could not be smoged, (In C.A. you have to pass a smog check to register your car.)
Minor cosmetic problems that should not be happening on the interior, IE. paint fell off of shifter, plastic on seat belt fell off, and the center console keeps coming loose.
The passenger side window won't seat correct and has a whistle.
The power window switch on the passenger side failed.
The air conditioner control panel was replaced three times in three years and in now starting to fail again.
Last, but not least I just found the the power steering pump is now whining and the fluid is disappearing with out a puddle under the car.
I have been a Chevy fan for a long time, but after this car I am in question on the quality of GM. I currently own a 1991 S10, (I have had it for 6 years), and am very happy with it. I find the Malibu very comfy on short and long trips. I also love the power, handling, and room of the back seat and large trunk.
My friend also has the same year Malibu, but he has the LS. HE has had most of the same problems and feels the same way as I do. Four days ago I traded in my Malibu in for a 2003 mustang GT. I loved every thing about the Malibu except for the constant problems here and there. I was always worried about what would happen next, and the warranty was up last June.
My Malibu also has many of the same problems. My water pump failed due to the "high mileage coolant" that we are required to have in our high performance machines. The coolant is too toxic and eats through the gaskets filling the engine with coolant and causing $1200.00 worth of damage. I also have had to replace my brake pads ever 6-9 months and I have tail lights that have shorted. My power steering pump is now whinning and I have noticed paint falling off of the interior and half of my dash light decided not to work. I would much rather spend extra money for peace of mind rather than a piece of junk.
I have a 97 Malibu LS and have had several of the problems you and others mention. As for the unexplainable Check Engine light, apparently a loose gas cap triggers that, and my sister with a 2001 Malibu has had the same problem. With 95,000 miles some more expensive problems are beginning, such as the front hub bearings needing to be replaced.
I am currently in the process of tearing down the engine of a 2.4 liter, 1997 Chevrolet Malibu. The water pump bearing failed, and dropped all of its ball bearings into the motor. This caused the timing chain to jump a few teeth. I have yet to find out whether this type of failure will cause damage to the valves and/or pistons, however, in my opinion, a water pump failure should not be allowed to cause this much trouble. There is no recall on this issue, but I believe it is something that needs to be addressed. I will post my findings shortly.