It depends on your manufacturing capabilities (minimum gap/line width) and mechnical tolerances.
Higher dielectric constant means shorter resonator length.
Advantage: small filter dimensions
Disadvantage: more sensitive to etching precision
Thicker substrate means wider lines, for the same line impedance
Advantage:
- easier to do high impedance lines, for a given minimum gap/line width (etching tolerances!)
- increased coupling to parallel lines, for a given gap width
Disadvantage:
- low impedance lines might be too wide
- long vias with higher via inductance (if you need vias)
- more radiation