In my kitchen I have:
1. A fridge
2. A coffee machine
3. A stove
4. A microwave
5. A blender
6. Mixing bowls
7. Measuring cups
All I want to do is feed myself. Why on earth do I need to have so many different things to do it?
</snark>
To...most people, having a separate "app" for things that do wildly different things is a good. Skype and email fill completely different roles to me, and I suspect they fill completely different roles to other people as well.
You might want to send a message to somebody and not care how, but I do care how.
If it's late, I might send my friend an email instead of an SMS because I know that the SMS will probably wake her up, and the email won't.
Being able to control this is a good thing.
Did you notice the descention of immediacy in your example of phone->sms->email? You went from the most demanding contact method "stop what you are doing and talk to me!" to the middle "stop what you are doing and read these 160 characters!" to the least "eventually look at this piece of text".
If you didn't care as much about your message, you probably would have done this in a different order.
If something major in my life happened (I'm having a baby! I'm going back to school! I got into YC! Somebody is buying one of my projects!), I would call my best friends to tell them, I wouldn't SMS them.
So would you.
And this is good.