You can't just throw software at this. It's a complex system that involves way more than just an airplane and someone in a tower. Systems engineering, human factors, and safety management systems are the relevant disciplines if you'd like to start reading up. In addition there are decades of research on the dynamics between human operators and automation, and the answer is never as simple as "just add more automation." Increased reliance on automation can paradoxically decrease safety.
CPDLC is already being deployed domestically. It's currently available to all operators in en route segments.
All runway incursions at towered airports are reported, classified according to risk, and investigated.
> You can't just throw software at this
Ok, let's not try improving systems, how's that working out?
On the flipside, look at the success of TCAS. It doesn't have a perfect operational history. It hasn't completely eliminated midairs, either. But it took a relatively rare event and further reduced the frequency by about a factor of 5.
I wouldn't be so quick to rule out that there's some kind of relatively easy technological double check that could greatly reduce incidents. The fact that we've not gotten there despite years of effort to reduce runway incursions doesn't mean that it's not possible.