It's missing fractional selection and per-layer alpha channels. With those two features, it would be almost usable. Without them, most photo editing tasks are highly difficult.

Fractional selection lets you apply adjustments and effects without harsh boundaries between the adjusted part and the unaffected part. Per-layer alpha channels are needed to blend together different layers smoothly. And actually, you could implement the effect of the former with just the latter.

So yeah; Paint.NET needs editable per-layer transparency channels.