Doing 2d in 2d vs 3d?

I'm new to Unity, so I'm looking for some feedback from the more veteran folks here...

I know that 2d support was improved with 4.3, but I've already noticed one thing lacking (Physics2d.IgnoreCollision and/or one-way edge colliders). This got me concerned over starting in native 2D, so I'm looking for the pros/cons to working with native 2D vs. doing 2D in 3D.

- Are there other gaps/gotchas in the native 2D approach, or is it pretty much just this?
- Are there bigger gotchas when doing 2D in 3D? (And I don't mean things like constraining Z for rigidbodies... I can handle that)
- Is Unity pretty good about closing gaps like this (is it reasonable to expect this gap closed in... say... three months)?

My inclination is to work with sprites and basic shapes in 3D, but it concerns me because I think "native 2D is *designed* for what you need... use it and have faith that it will work/be patched 'in time'" (It's not like I'm working on the Mona Lisa of video games here... it'll just be a Super Crate Box clone to get familiar with things... though I'd like it to be complete).

Any feedback is appreciated.