The things Click with Ethernet or Click Plus does better than Micrologix 1400:
1) All comments stored on the PLC
2) MSG instructions can be edited live (Send and Receive instructions)
3) PID instruction is better, although I think you are limited to fewer of them. The scaling is superior and the Click Software has an Auto-tune that worked great the one time I used it so far.
If I may:
4) The high speed counter is way easier to configure
5) Can be added to the I/O tree of a Compact/ControlLogix
6) The program logic is stored in flash so a battery failure won't cause the program to be lost. However, the data will be lost so you'll have to write a routine to detect the battery failure and write in at least some default values for everything. Still an improvement