Make certain that all of the Apple applications are updated to their latest version supported by Mavericks. Update any third-party applications to their Yosemite compatibility versions. If you have third-party kernel extensions, or frameworks installed, these need to be current for Mavericks, and preferably Yosemite or El Capitan if available. Key stumbling blocks will be printer and scanner driver support. Look at that closely to see if your vendor(s) support Yosemite and El Capitan. Drivers that state 10.6+, 10.8+ are suspects.
Remove every trace of anti-virus/anti-malware, and so-called cleaner applications. If you use Finder replacements, they may break in El Capitan because it uses System Integrity Protection (SIP) to block changes to the operating system.
I know that Yosemite and El Capitan expect iPhoto 9.6.1, and they may also expect the last available aperture release too. Otherwise, Photos may fail to migrate your iPhoto/Aperture database. You may want to check in the iLife (iPhoto) and Professional Application (Aperture) communities for additional information on the results of an El Capitan update.
Since I performed a clean install migration from Mavericks to El Capitan, I cannot comment on the upgrade process. I can say that installing El Capitan into my 2011 Mac mini Core I5 with SSD is turning out to be a 10 second boot to Desktop, and everything is better, faster, and more stable than Mavericks. Since I use a networked Samsung printer, I didn't bother loading drivers. I keyed in its static IP address, the printer model was detected, and El Capitan went out on the Internet and got the correct drivers. Just works.