- C1 definitely shouldn't be there. It disconnects V+ pin from the actual power line. Probably you meant to place it between V+ and ground
- Crystal resonator is supposed to be connected between X1 and X2 pins, not between X1 and the ground.
- U5 probably needs its own crystal between OSC1 and OSC2 (or clock source, check with datasheet)
- If R1 and U1 are meant to form a voltage divider, R1 value is too small. (same goes for R4) Proper value should be roughly the same order as U1 resistance in normal operating conditions.
- In general, the situation with op-amps and MOSFETs is not too clear. Are you trying to achieve voltage repeaters? Or amplify the signal? This can be done a lot simpler without the need for any transistors and will also produce cleaner signal. I don't see any reason why soil probes should be its own circuits (as for your update) If they are just some kind of variable resistance that seems to be enough here. (Only with proper R1 R4 values)
- SDA / SCL lines are not connected correctly. You need SDA/SCL lines going directly from arduino to U6 and both of then pulled-up independently to VCC.
- SPI bus seems to have 2 devices connected but no way of actually switching between them two. (CS pin is hard-wired to ground) This is related to your question #5 If you need to connect 2 devices to a single SPI bus, you need to wire their CS pins to your arduino GPIO lines and use that to switch them at runtime.
- Getting a 24 bit ADC doesn't automatically make your circuit 'precision'. You need to take a lot of care with power isolation and smoothing. Simply sticking power line info VREF is definitely not enough. So either your ADC is too powerful for this task and you don't really need all that precision or you need to properly insulate analog circuitry from the digital noise. That's a big topic on its own.
"Which capacitors are bypass, blocking or coupling?" - is kinda odd question to ask. It implies that you first randomly slap a bunch of capacitors on and then ask what is their purpose?
Conclusion (based on comments and other's input): Just use Arduino and plug your sensors directly into it using proper R1/R4 for voltage dividers.