RTD sensor circuit design
DIN standard 100 ohm RTDs are 100 ohms at 0'C and 138.50 ohms at 100'C. 

Starting at the beginning, your switched current sink looks quite inadequate. You need it steady to within +/-0.03% for 0.1'C, and it depends on the (noisy) GPIO voltage of a micro vs. the (poorly defined and temperature-sensitive) Vgs of the MOSFET Q1 (and the matching to Q2, and some other stuff). Wrap an op-amp around the current sink for sure, and give it a proper reference voltage, not the supply voltage of the micro. 

Even if you have a so-called rail-to-rail op-amp you should not work right to 0V and 5V if you actually are required to read those corresponding temperatures. Knock a bit (depending on the op-amp) off each end and live with reduced resolution. 

As far as EMI susceptibility goes, you should put some low pass filtering ahead of the amplifier. 0.1'C is about 38.5uV DC which is a rather healthy signal at DC, but it's easy for noise, hum etc. to creep in. 

Whether self-heating is an issue or not depends on the time constant of the RTD in the measured medium (including whatever protection tube or other materials are present) vs. your measuring time (probably you want to average a number of readings). 

I would suggest not switching the current to the RTD unless you have some reason to do so. It will just cause a small offset that is relatively stable.