I disagree about the sound quality of aftermarket HU. "a proper amp and eq" can't fix a poor source (e.g. speaker-to-line level converters)
Without discussing unique one-off alternative's (like SN's adaptation of home audio rack-mount processors), a HU with proper 4, 6, or 8V line outs will be a better source from the beginning.
And some of the "flash" is no longer just flashy crap like dancing lights. HU's often have true parametric EQ's and crossovers built in, crossovers built-in for your line-outs, and new android HU's have the ability to run apps - I'd love to have an android HU and run the Torque app to have my gauges for coolant temp, AFR, boost, etc, right there in the dash.
Losing the OEM integration like the display panel is a definite drawback. There are adapters made to enable use of factory steering wheel switches - though there have been a few threads here about issues with them, IIRC.