That depends on whether or not you want to design an engine to produce a game to be done in three years, or one year or six months, and whether or not you're thinking of console ports. It'll be relatively easy to throw out a 360 port of your game from Direct3D9, but you'll need to do a lot more originating from D3D11. Remember that D3D11 locks out all XP users, if not necessarily all D3D9 hardware.
The most recent Steam survey suggests that about 16% of people still use Windows XP. Can you afford to cut them out? By the time your game is done, how will this have changed? Are you going to use features that depend on the higher level API? These are questions that you will need to answer yourself.
Direct3D 9 is pretty damn accessible and you can reach a lot of people with a D3D9 game, but it's days are numbered, especially on the PC. If you're not interested in targetting those people, then there's little point to it.
Oh, and don't bother with DX10. There's no reason at all to use it over DX11. Unless you want to use D2D/DirectWrite, which is not unreasonable.
Of course, it's worth mentioning that in DX11, there are no replacements for classes that, as a hobbyist myself, I found extremely useful in DX9. Such as ID3DXMesh, ID3DXSprite, ID3DXFont, have to compile ID3DXEffect from source, etc. Microsoft recommends DirectWrite to replace ID3DXFont, but of course, they forgot to actually make DX11 compatible with the new Direct2D/DirectWrite systems, which in my opinion was blindingly stupid.