I already answered some of the questions in the DS News forum. Use v0.4 Beta for Illusion of Gaia and turn off speedhacks to get past the title screen. Toggle the Vblank settings (normal speed vs fast speed in v0.6 alpha) to make the SMW bosses workable.
I'll elaborate on what I was talking about earlier. You see, emulators for the PC do much of their work in the background, using up lots of CPU time. They calculate exactly what happens each frame, what the screen should look like after that point, and then paint the new image to the screen pixel by pixel, doing the whole thing 60 times per second. That's fine on the PC where you've got tons of processing power to work with, but on the DS this would not be feasible. It would work, but you'd be getting horrendous speeds, and probably no sound. The SNES emulators for the PSP use this method, but they've got 333 MHz to work with. The DS has two processors at 66 MHz and 33 MHz, the second being used solely for audio emulation.
Rather that using this method (called "software emulation"), the SNES emulators for the DS use the DS's native 2D hardware to speed things up. Rather than calculating what the screen should look like in software, they receive the SNES graphics instructions, quickly translate them into DS 2D hardware equivalents, and blindly paint the graphics to the screen. This greatly reduces the amount of time it takes to render the screen to only about 5% of the CPU time, but it also introduces graphical problems. Because the DS's 2D hardware does not match up exactly to the SNES graphics hardware, some errors occur, especially with transparencies and layer priorities. In addition, the DS doesn't have enough layers to fully emulate all the possible layering configurations the SNES could have, which causes additional problems. You can use the Graphics config menu to work with some of these issues, but not all of them can be fixed.
I haven't heard anything from Archeide in a few months, but keep in mind he's working on it on his own time. Looking back at his first releases, the fact that it's working as well as it is is already a major accomplishment. Maybe he's stopped working on it, maybe he hasn't. He did state long ago that once he lost interest in the project he would stop updating it, so perhaps we've reached that stage. Who knows?
There are two other SNES emulators available for the DS. The better of the two is SnezziDS, but it does not run on slot-1 devices. You can test it in no$GBA if you want to see how it works though. The other is SNES DS, which has not been updated since late 2005 except to add DLDI support. While it does work well for many games, you cannot configure the graphics layering at all in-game, and the default layering doesn't work too well. Due to this, the best method is to apply the layering settings found in the latest snesadvance.dat file by packaging the SNES game directly into the *.nds file, but after Loopy added DLDI support he removed the tools needed to do this. I could upload them if you're interested, but honestly it's probably not worth using SNES DS for most games.
EDIT: If you wish for a comparison between hardware vs software emulation, test the following:
1. NesterDS vs NES DS - NesterDS uses software emulation and is more accurate graphically, but requires frameskip just to maintain full speed. NES DS uses hardware rendering so it can run really fast.
2. HW vs SW renderer builds of jEnesisDS v0.4a - this is the same version of jEnesisDS but with both a hardware and software renderer. Notice how the software one requires 2-4 frameskip to maintain full speed, while the hardware one doesn't even offer frameskip because it wouldn't help at all (again, only 5% of the CPU time is spent drawing the screen with hardware emulation).
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