My Subaru is heavily modified and running a tuned factory ecu
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I honestly didn't notice any difference in mileage. Fueling is set at stoich and stays there for non-performance driving. As for timing, at lower rpms where hypermiling takes place, my factory settings were already pulling a few degrees of timing from knock detection so there were no gains to be made unless even higher octane(currently at 93) is used.
On modern naturally aspirated engines there also isn't much to do to increase fuel mileage. Most of them are already running at max timing with low octane at stoich fuel, so upping the timing or fuel octane would only result in losses.
I suppose, if the engine was drive by wire, you could limit the throttle to 50% max, or set the rev limiter to 3,000rpm. One area that hasn't been explored much is cam timing. Many newer engines have computer controlled variable cam timing.
Most off the shelf tunes are very conservative to compensate for the differences in engines. My engine doesn't like much timing, but I've seen others with the same motor and similar mods run 5 degrees more with no problems.
Tuning equipment drives the cost of really quick. You need a wideband o2 sesor, and should have an egt gage. Then there's the tuning software. Subaru's is free, but any other make is $$$$. As far as saving money, you'll have to find a once in a lifetime deal to make engine tuning on a modern car pay for itself.
Manyt stand alone fuel computer are MAP based. Most modern factory systems are MAF based. MAF is more accurate for fueling. Moving from an old factor MAP based system to a newer MAF based system would probably see gains. Honda owners might be able to do that.
Emission aren't a problem unless you are missing cats or running a huge cam. In many instances a factory ecu can be kept in place while using an aftermarket ecu to do the real engine management(utec, aem).
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