One major issue is that radar doesn’t work very well at low altitudes. The lower you aim the beam, the more ground clutter you pick up (trees, buildings, clouds, etc).
ADS-B helps with this as it's self-reporting. And systems like ASDE-X are useful to track objects once they hit the ground. But low-altitude deconfliction is a big problem.
One problem for sure is that when you're close to the ground you have to be careful about buildings, cell towers, etc. Terrain is one thing, but when you're a few hundred feet AGL, you could quickly be in the way of tall structures if a TCAS alert goes off.
(By the way, I believe EGPWS would take priority over TCAS anyway.)