first you need to define what do you mean by

make it "smart"

...the accuracy of the ADC on the ESP32 is very important...
well... ESP32 is a general purpose MCU integrating a lot of digital peripherals and on top of these a RF frontend. You cannot expect the integrated ADC which is an analog peripheral, to have similar performance like a dedicated ADC chip ...

well, I don't want to add salt to the wound, but who took the architectural decision without having an answer to these basic questions...
I look around for some engineering documents, but couldn't find anythng beside marketing materials. I'm also curious about this communication "beast".
Maybe ...

AFAIK, ESP32-PICO-D4 is a module while ESP32-S3FH4R2 it's a SoC only. SoCs do not have anything around so the answer is no.
You might look to ESP32-S3-WROOM-x which is a module and has the external crystal.

Well … this is not quite a wiring diagram, but rather a high-level introductory slide.
At high level, it looks ok, but as you know, the evil is in details which are missing

I wanted to show how reset and boot signals are generated from CH343 DTR/RTS, but cannot add a picture here because this error
"Sorry, the board attachment quota has been reached." :(
...maybe a forum moderator can help.

It looks, when cable is disconnected, you are in the state with DTR = 1 and ...

Give us some more hints on your usecase and scenarios, like what you try to achieve, what you want to measure/monitor, what types of sensors, connection type, communication needs... and we might give some ideas. Otherwise its hard to come with something.

1. There are no constraints for GPIO12, GPIO13 so its safe to use them for i2c
Strapping pins for S3 are, according to the datasheet, GPIO 0, 3 45 and 46
2. Internal pull-up/down, according to the same data sheet is 45k, so too high for I2C

Obviously, my assumptions are wrong 😊
It looks to be a normal dev kit with 2 usb connectors and no usb hub.
I could not find the schematic for this specific board but looking at the pictures I would expect it follows standard ESP32-S3-DevKitC-1 (https://docs.espressif.com/projects/esp-dev-kits/en ...

..but I would remove R5, R7..

what i mean, is to replace those resistors with 0 ohm value, not to effectively remove them.
for capacitors yes, remove means remove.
Sory for confusion