iMessage is apple's text system. This only works when texting messages between apple devices which both have iMessage switched on. When someone texts you, the message will go to all your apple devices which have iMessage switched on. However, this will not work when someone texts you from a non-apple device ie not using iMessage. In such instances, your iPhone will use the traditional text system and not iMessage. That is why some messages will only go to your iPhone.
I hope that this makes sense.
Do you want to see all text messages on the iPhone, or none?
Using FaceTime http://support.apple.com/kb/ht4319
Troubleshooting FaceTime http://support.apple.com/kb/TS3367
The Complete Guide to FaceTime + iMessage: Setup, Use, and Troubleshooting
Troubleshooting FaceTime and iMessage activation
Using FaceTime and iMessage behind a firewall
iOS: About Messages
Set up iMessage
iOS 6 and OS X Mountain Lion: Link your phone number and Apple ID for use with FaceTime and iMessage
How to Set Up & Use iMessage on iPhone, iPad, & iPod touch with iOS
Troubleshooting iMessage Issues: Some Useful Tips You Should Try
Setting Up Multiple iOS Devices for iMessage and Facetime
FaceTime and iMessage not accepting Apple ID password
Unable to use FaceTime and iMessage with my apple ID
How to Block Someone on FaceTime
My Facetime Doesn't Ring
To send messages to non-Apple devices, check out the TextFree app https://itunes.apple.com/us/app/text-free-textfree-sms-real/id399355755?mt=8
How to Send SMS from iPad
You can check the status of the FaceTime/iMessage servers at this link.