Well, you seem to know all there is to know
The key thing - Reduce overdraw as much as possible. Overlapping sprites = really bad.
There is one more optimization you can do, though it is not automated in tk2d as it is harder to control and won't work in all cases.
Lets say you have a bunch of sprites which are predominantly solid with feathered edges or something. What you do is split up the texture into 2 textures, the first being the solid bits only - 1-2 pixel edge, and the second is just the feathered outline. All you do is go into photoshop edit the alpha channel and cut out a huge alpha hole where the solid bits are in the 2nd option.
In tk2d, make sure dicing is turned on for the second texture - it will nicely get packed into small thin polygons, and the first doesn't need tiling if its rectangular. On the first, override the material to a solid material (tk2d/SolidVertexColor) (
http://unikronsoftware.com/2dtoolkit/doc/tutorial/multiple_materials_in_a_sprite_collection.html). Now you can create a composite sprite, they both should have the same parameters & anchor, so will perfectly complement each other when placed at the same location.
If you have a bunch of sprites which are mostly solid, you will save a TON of fillrate this way.