Reading all this talk of "dealing with" actual hardware is a little disappointing.
I guess perhaps living in Europe (easy access to RGB) and being able to mod my own consoles (no shipping hassles, chasing modders, low cost...) might skew my view but I'm really quite passionate about playing on original hardware.
FPGAs are neat an all but have as much appeal to me as emulation I guess.
There's a pretty big wall between starting fresh and where we are now. There's a lot to absorb and a lot of skill needed (I mod all my own stuff too) that I don't think most people have. If there's an easier solution that gets you 98% of the way there, analog included, with extremely good implementations for NES and pretty damn close for just about anything else up to a certain point, then sure I think that's perfectly OK. I wouldn't sell my stuff and start over with that right now (I also don't like wasting my time selling stuff, it's not worth the money for the hastle) but if someone had that and was dissatisfied with something, adding on real hardware from there isn't a big deal. The same way I have traditionally argued starting with a Wii + Virtual Console and adding from that is pretty cool, and an FPGA system is miles better than that.
I tried to explain what I did to get my NES setup to someone at work (AV Fami, NESRGB I put in myself, RGB cable, FM, everdrive, FDS ram adapter + FDS stick), but when he got to "do you think it's worth it" it gets hard to justify for people who aren't me. I'm also pretty fortunate to not have to worry about import fees for expensive purchases from Japan. And like where I'm at now with a lot less spare time it would be hard to justify if I was starting now with none of this stuff.
I've even invested in better modding tools. I bought a Hakko FX-888D (~$100) to get better temp control and better tips, justifying it by saying I'm not going to fuck up my $300 PC Engine because I cheap'd out with a $10 soldering iron. I even finally bought a proper dremel.
And like I said there's some stuff that just isn't going to be replaced. You're not going to see an FPGA take on a Windows 98 compatible computer, ever, guaranteed. Just way too complicated. But maybe someone could do an MT-32 implementation, that would make me pretty excited.