I own a lot of flashcarts. A lot of them. I own almost all of the Everdrive line. Couple quick points here:
Unfortunately, you can't just harvest the various special chips and put them on a SNES board. The only one you can do that with is the DSP. The SD2SNES doesn't actually have any of the SNES's special chips on-board, rather it uses an FPGA to recreate them also. At this time, the SuperFX chip isn't done, nor is SA-1 (which is what knocks out SMW2 and SMRPG) or a couple other very minor chips. But ikari appears to have started making some real progress on it, so who knows what tomorrow will bring, that's the nicety of firmware updates on the more expensive games.
The Everdrive N8 for the NES/Famicom is somewhat similar. It didn't use extra chips per se, but it used mappers. The majority of the mappers are working (or in the case of MMC5, working "enough", kinda like emulators, to have Castlevania be playable) at this point, but not all of them are 100% perfect. Krikzz is working on them continually, but he does have a whole ton of other products to support.
As far as flash carts for other systems I own...
Like Wiggy said, if there's any difference between "real" and flash cart on the TurboED, I can't see it either.
The Everdrive 64 supports almost every game, with a few wonky problems with saving (and I mean very few. Like, count on your hands few, and most of them I would call playable just slightly temperamental)
The Mega Everdrive (for the Mega Drive/Genesis) sure seems to play everything as far as I can tell, including 32x games (if you have a 32x) and Master System games (assuming your 32x isn't plugged in -- Genesis hardware limitation, not flash cart limitation). It even works to save your SegaCD games or as a bios chip override for the SegaCD. (Note: I have been told the bios override isn't perfect, but I have never had a problem) (Second Note: I am talking about the Mega Everdrive, not the Everdrive MD. Krikzz makes 2 different Genesis flash carts)
The EverdriveGG for Game Gear has never given me a problem. I'm told it plays SMS games, but honestly haven't tried.
The Master Everdrive for SMS, same.
Non-everdrive flash carts I own:
The Harmony cart for the Atari 2600 plays something like 99% of commercial games and most homebrew, and batari's coming out with the Harmony Encore to bump it up to 100% of existing games
The "Ultimate SD" carts for the Atari 5200 and Colecovision both appear to have 100% retail compatibility
The Flashboy+, same. Playing Street Fighter 2 on my Virtual Boy is amazing.
The VecFlash for the Vectrex is a little tweaky, but again seems to play all retail games.
Uhh... I think that's it. If I see any more, I'll edit later. I'm way past what you asked about anyway, I just love my flash carts and enjoy giving recommendations whenever I can. There's others I don't own, either because they're out of production (Skunkboard for the Jaguar, CuttleCart for the Intellivision and Atari 7800) or because I'm waiting for a better/more elegant solution to come out (FlashMasta for the NGPC, EZ-Flash 3 for the GBA, a handmade Lynx one sold on Atariage that I'm not even sure has a name -- I usually prefer SD-based carts), and I own a very respectable collection of physical carts, but for homebrews, translations, hacks, and the occasional "Dear LORD that's expensive but I'd really like to play it on the original system", you cannot beat modern flash carts.
