I'm going to try to give some very explicit and clear cut answers because I have always wondered about parts of your questions as well.
So we have a common discussion point for frames of reference:
Wikipedia words it this way,
All inertial frames are in a state of constant, rectilinear motion with respect to one another; they are not accelerating (in the sense of proper acceleration that would be detected by an accelerometer)...In general relativity, an inertial reference frame is only an approximation that applies in a region that is small enough for the curvature of space to be negligible
http://en.wikipedia.org/wiki/Inertial_frame
Notice there is NO reference to a particular type of reference frame. I'd loosely define "proper" here as meaning "local" for this discussion, but it has a more specific definition.
A local reference frame is explained this way:
The term is most often used in the context of the application of local inertial frames to small regions of a gravitational field. Although gravitational tidal forces will cause the background geometry to become noticeably non-Euclidean over larger regions,
http://en.wikipedia.org/wiki/Local_reference_frame
Again note it is space (time) to which curvature criteria applies, not the selected coordinate reference frame. Eucledean space is flat multi dimensional space and we can use Cartesian( or other) coordinates to define our measurement parameters..."non-Euclidean" means curved space time.
To your questions:
According to the definition of a "local inertial" frame in GR, you must use a coordinate system that locally looks Cartesian, right?
From the above we can conclude, "No". You can use ANY convenient coordinate system...Cartesian or polar or spherical for example.
I mean if you had a coordinate system with a basis that wasn't orthogonal, then it would not be considered a local inertial frame, right?
"No" again because it's the motion of the coordinate system not its type (Cartesian or Polar or spherical or cylindrical) that makes it inertial or not. You can usually use coordinate transformations to get from one coordinate system to another, say: x = r cosθ and y = r sinθ to go from polar to Cartesian. The Lorentz transformation in relativity is a special one used for homogeneous space
I ask because outside of relativity, I would normally say that whether a frame is inertial or not wouldn't depend on the coordinate system you choose. If your frame is in uniform motion, then it's inertial regardless of which way you point your meter stick.
This is accurate inside relativity too. You last sentence here says it all.
In general relativity, an inertial reference frame is only an approximation that applies in a region that is small enough for the curvature of space to be negligible. So space is curved over larger distances but we keep our observations to only a small region...analogous to how we measure a mile of highway via GPS,for example, as if it were flat even though there are 'ripples'..hills, valleys, and curvature of tghe earth.
edit: "Long range" measurements [in curved space] have unique problems...see my next post.