Check and Balances?

The news that Supreme Court Justice David Souter is planning to retire, started me thinking (yes, I know...quite dangerous, or at least annoying). If the three branches of Government are supposed to be independent, how come the President can pick his Supreme Court Justice? Sure, Congress still has to approve, but if both the President and Congress belong to the same political party, won't the Judge also be of the same ilk? Doesn't that slant Government to one view only? So much for the two-party system and checks and balances. Can anyone out there supply an answer to this quick question? Please post back a comment if you can. Thanks.