aftermarket remote starters will always give you the best quality and features if they are a quality brand, at work i install nothing but compustar pro 9000 series and have less than 1% return rate. when we were installing Ford rmst systems we had nothing but problems because they are cheap pieces of crap.
and if you use a aftermarket rmst you DON'T lose a second key if the installer puts in a good transponder over ride kit. i use www.idatalink.com
data kits for all our installs.
also your warranty will not be void with a aftermarket rmst system, unless the root cause of the problem is the rmst system, so if you get a crappy install and it causes problems then you may have to pay to get it fixed, but if it is installed properly all connections soldered and connected correctly you shouldn't have problems.
i do 300+ installs a year and not once has a customer be denied warranty.