That's all fair, I definitely see the appeal (especially regarding the controllers, which is something third-party companies have struggled to get right for decades). They're a good way to play the games. But for me at least (and I've heard similar sentiments from others), a big part of the "retro experience" comes from playing on a real console and a CRT TV. Something about the built-in firmware and knowing it's basically just a raspberry pi under the hood puts me off the whole thing and I would rather just emulate on a PC because it's less hassle. But ultimately of course if you enjoy it then keep doing so!
Oh, sure, they're no substitute to a "hardcore" retro gamer. Folks who won't be happy with anything short of an FPGA recreation (if not original hardware) outputting to a Sony Wega, or a powerful modern computer getting a real workout doing fancy render-ahead tricks to fake real-hardware input latency (so: remarkably low, by modern standards) and neat multi-step high-fidelity CRT-mimicking shader output, won't be satisfied by the classic consoles. But they're damn good for what they are, and especially for folks who don't know WTF an emulator is, or do but don't want to mess with them—the Nintendo ones, at least, the rest seem to have fallen short on one or more important measures.