Junction to ambient figure means in simple terms how much does the semiconductor heat up in relation to ambient temperature given a specific power dissipation in watts. so \$100 \frac{°C}W\$ \$T_a=25°C\$ with 1W of dissipation leads to 125°C temperature.
This obviously depends on available copper area to dissipate heat, copper thickness, thermal vias to use the opposite side of the PCB for heat dissipation and so on. You may even use a solder-on heatsink for SMD chips which boost the dissipation a fair bit. Or the more traditional glue-on solution.
In short, less thermal resistance equals better but as others pointed out, the better thermal conductive part has much lower max temperature so it's a bit of give and take.
A better metric than \$R_{\phi JA}\$ would be \$R_{\phi JC}\$, temperature from junction to case (or pad). After all, at that point it becomes your job to dissipate the heat one way or another. Plus it's not up to whatever PCB technology / pad style you're using.