If you have the storage room on your recorder, I'd always recommend using the highest quality available. That way you'll always have the best possible master recording, you can always down-convert later on depending on your destination media.
24-bit resolution doesn't really get you more nuances per se, but it does increase your audio capture dynamic range. If you are recording quiet sounds, or sounds with dynamic (or unpredictable) levels, using 24-bit can benefit your recordings by significantly lowering the digital noise floor. In that sense, you will better be able to capture quiet sounds (and boost levels later on), which could be said to allow for more detailed nuances. For nature recordings, which are often unpredictable and quiet, this would be a good idea.
96 kHz doesn't necessarily help you as much in this case, unless you're trying to capture super sonic sounds (you'll need a microphone that can capture these frequencies as well) which can occur in nature, like sounds of bats. However if you plan to apply post-processing on the sounds, or perhaps slow them down or do some creative manipulation, 96 kHz will help you accomplish that with better quality results.
Using external condenser microphones is typically better than the built-ins in the case with all digital audio recorders (not saying the built-ins are bad). If you have access to external mics I would use those, and even do a sound test between them to see what sounds better to you and with your equipment.