I only want the phone to keep the phone numbers. If I try to enter a name and phone number combination, and I enter the name with any slight variation with the name of that person retrieved by Android looking at Skype or e-mail, I will have a duplicate entry for that person (in some fora, people complain of having several entries for the same person).
I can't believe that there is not a simple way to do it; the current one looks (at least to me) inefficient and a mess. Hate to have to deal with it.
One thing I like about the Android platform is that it is very customizable. Because much of it is open source, people can modify it to meet their needs, and we can benefit from the modifications of others. I don't think you'll find that on any other platform, so Android is probably as good as you're going to get.
That said, it's not yet clear to me how you'd like it to work. If you could explain it here, perhaps I or others can recommend some customizations. For example, one thing that irritated me at first -- maybe this is what you're talking about -- was that the Contacts app seemed to list every contact address (including email addresses), but I don't send email from the Contacts app, so I changed it to list only those contacts that have phone numbers.
Also, there are a number of replacement contact list apps in the Play store. I've tried a few, but I'm able to make the stock Contacts app work well enough for my needs.