I walked into Nick's barn a few months ago and said.... WHOA, who's motor build is that??? I guess I was looking at yours man! It's going to be an insanely good motor. I'm excited for you. Please share (or put up a build thread) when it's in the car. In any case, you have the ability to overheat the stock cooling system better than any of us so i'm curious what radiator you're using now (OEM?).
BTW, I updated the thread above with my 0.02 pesos.
Before I go into HKS vs. other EMS's... Let me say, your tune is only as good as your tuner. Secondary is the equipment he has to work with. You also get what you pay for. With that said, the HKS systems are much more expensive. Again, the theme to my build was not to find the cheapest components but to find the best value. I struggled with AEM FIC vs. AEM EMS vs. ProEFI vs. HKS F-Con is vs. HKS F-Con Vpro vs. Motec. To me the HKS was the best value by a long shot. Notice I did not mention the AEM Infinity 10. I hear that system was a complete overhaul of their software and hardware. I would consider that if I was in the market now.
In general HKS has very good hardware and software. AEM was known to have buggy software requiring a lot of updates and a lot of warranty returns/refurbish.
In terms of piggybacks.. you can't compare the AEM FIC between the HKS F-Con iS. The FIC is so old now. AEM has pretty much ignored that platform for maybe near a decade. It's like a Motorola Startac phone vs. a Nexus 5. The AEM is a basic fuel injector controller. The HKS iS controls ignition timing (you can advance the timing), controls the injectors, reads all the OEM OBD1 and OBD2 factory Honda sensors (Throttle Position, RPM, Coolant Temp, MAP/load/boost, Speed, etc). The HKS also has many more available trim maps. Those trim maps are also more granular and precise. It's a pretty amazing "piggyback". It can even Autotune for those brave guys 
The reason why HKS isn't very popular here is because of the dealer support and their proprietary software. Its not an "open" platform like the AEM which any Civic owner can tinker with. More about the features of the iS here.
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The iS series is HKS's correction / trim only ECU.
It features:
• 4 24x16 INJECTION trim maps (8x in total, for AFM or MAP), for different fuel octane ratings.
• 4 24x16 IGNITION trim maps (8x in total, for AFM or MAP), for different fuel octane ratings.
• 24x16 INJECTION and IGNITION trim maps, for scramble mode.
• 12x8 INJECTION and IGNITION correction map based on throttle change and RPM.
• 24x16 INJECTION correction map, applied by AFR-target map.
• 24x16 AFR target map for wideband-controller feedback correction, applied to the 24x16 fuel trim map.
It also features 2 optional voltage outputs suitable for:
• Airflow.
Injection (fuel) and ignition (spark) trim and correction can be individually enabled and disabled by:
• VPC
• Throttle change correction map
• Scramble map
• GCC (graphical control computer)
• IAT correction map
• ECT correction map
• Fuel trim map A
• Fuel trim map B
The iS series also features a cool feature that does not require having the optional Navigator unit. Basically there is S-Video output to display specs and numbers to a mini-TV, a popular item in Japan and slowly becoming popular in Australia and elsewhere around the world.
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Also Ben, HKS is a huge company in Japan. They consult for OEMs a big part of their revenue stream. They bought from Honda the NSX ECU code base which is why the iS can read all the OEM sensors even on the OBD1. There are also many happy AEM EMS people (not sure there are many happy FIC users though, and of the happy ones, i'm not sure how hard they really drive their NSXs). You get what you pay for but I don't think the EMS unit is "bad" per say.
