The main Dialer screen defaults to your Speed Dial and your most recent calls, because that's what many people would be most interested in. If you'd rather see your entire contact list first, go to the People app instead, since it's very easy to select a contact and call them from that app.
You don't even have to go to the People app. Just tap the Google Search bar, and start typing in a name. As long as you have Google Search set to search your People app (along with the web), it should bring up the contact you're looking for quickly. Select that contact, and choose to make a call.
Not sure what to tell you about the contact lag--I actually experience none on mine. Lag issues can sometimes be resolved by booting into Recovery Mode and wiping the system cache partition (which doesn't erase any personal data). Be aware that this process can take upwards of 10 minutes on a Nexus 5:
http://forums.androidcentral.com/nexus-5-rooting-roms-hacks/352008-guide-nexus-5-recovery.html
I actually like Hangouts a lot. It's how the Ambassadors communicate with each other. It's essentially Instant Messaging that can be done anywhere you have access to Google. But you can also integrate your SMS into it.
The customization of Android is one of its greatest strengths. Most apps that have been downloaded a lot and have good reviews won't make your phone unstable or eat up too much battery, so give them a try. You can always uninstall them. Read the reviews before installing to make sure there aren't common issues that people complain about.
Don't worry--any new system has a learning curve. It'll become second nature soon enough.
