I would suggest a cautious approach to installing Yosemite:
- Clean install, don't upgrade on top of 10.9.5.
- Do a SMC reset and PRAM reset after installing Yosemite.
- Don't use migration assistant.
- Don't copy over system and library files from 10.9.5.
- Don't reinstall everything all at once. This will give you a chance to find any apps which could cause an issue with Yosemite.
- Only manually copy over user data that is needed. Leave the rest behind.
In fact I would suggest creating a second partition on your boot hard drive and clean install Yosemite on it. Play with the basic Yosemite and see if it performs well for you. This way you can always delete the partition when you are done.