I would start with a few NANO's
I like the two NANO shields that offer different wiring. one has screw terminals. the other has lots and lots of pins.
as for the high pin counts, look at two NANO's, they can talk and control at the same time.
the Beauty of the UNO is the shield use.
Getting two UNO's offers one for your display and one for a RTC board with SD card.
As a note, for an indoor garden, your temperature control could be by DS18B20, a simple to use, 1-wire sensor. the 1-wire bus can hold more sensors than you might need. these come in 1meter, 2 meter and 3meter cable legnths if you look around for them.