I would consider FD2-R wins hands down. Reliability comes with less cost of maintenance. The following 2 things are always of the most concerned of all, strictly make comparison by reliability and cost.
Engine: K20A wins
Simply because GTI has one more animal under the hood to take care of: the snail
Gearbox: traditional manual transmission wins, ie FD2-R
Though not the fastest, but it is the most tested, easiest and cheapest to maintain.
Spare parts: Jap wins.
I think this is very obvious to many. Besides not all mechanics know to handle German cars. But those can repair Jap cars are surely many time more. And Japanese spare parts are easy to source.
Besides, maybe the price parity between RON95 and RON97 makes FD2-R less attractive but I would still say Civic FD2-R is at the top of the chart.