I have a 2006 Civic I bought new and love with about 80k miles. You should keep it. Some important things:
1. Most shocks shouldn't need to be replaced this early. What makes you think they are done? Sleezy mechanics will tell you this to try to gouge you for uneeded work. You can also do it yourself and save some money.
2. The clear coat failure is a
manufacturing defect that was recalled. You could have got it replaced for free, but have missed the window.
http://www.thecarconnection.com/news/1092810_2006-2013-honda-civics-will-get-extended-paint-warrantyMy car did it along with 3 of my friends. I missed the recall period by a couple months, but Honda still paid half. It is worth having done as it only gets much worse. Go to a deal and ask if Honda will work with you on it as you didn't get notified.
3. This is a installation problem, take it back to the dealer that installed it and have them fix it for free.
4. Break pads are consumable. Change them yourself for $20 a piece from Autozone and you can take them back for lifetime replacements.
5. Snow, yes this car is poor in snow. However, a lot depends on tires. Put snow tires on and it fairs decently. It will never be an all drive wheel vehicle.
My civic has been a dream to maintain. Working on it is such a breeze compared to my wife's subaru and friends vehicles. Mine has been through three significant accidents and just keeps on trucking (only one with me driving and other two was other drivers fault).
Edit: That site about engine problems is kind of bias. Civic is one of the most common vehicles out there especially that year, so yeah there are going to be reports of engine problems. Given the millions that are out there and only 159 reporting engine block crack?