I've been doing a lot of thinking about this. I ordered a few of these pads for myself a few weeks ago but they still haven't arrived. The anticipation is killing me, I want to get in and try modifying them straight away, and I'm almost tempted to butcher my original Sega 6-button pad just to try some of these ideas.
I've read through the Hired Guns and ADoom manuals on the subject of modifying Sega pads to use more buttons. Hired Guns allows you to use the A, B, C and Start buttons. ADoom definitely supports X, Y, Z and Mode as well, according to the docs:
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The button mapping is as follows:
Start = Space (Action)
A = Strafe Right
B = Fire
C = Strafe Left
On the 6 button controller you also get
Mode = Esc (Menu)
X = Return (Enter/Show last message)
Y = Shift (Fast/Run)
Z = Tab (Map on/off)
A Sega Genesis controller may be use on the Amiga as long
as you swap lines 5 & 7, and put a 470 ohm resistor
between lines 5 & 7.
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I had a look at the pinouts of the Amiga and MegaDrive controllers, and the main difference is the +5V on the MegaDrive is on Pin 5 and on the Amiga it's on Pin 7. Swapping these around, (and adding a resistor for safety I guess) puts the +5V in the same place, allowing the extra buttons to be used if the software is looking for them, similar to how lowlevel.library understands the extra buttons on a CD32 pad. Unfortunately none of the data is the same between the MegaDrive and CD32 buttons, so doing this simple mod won't let you use any of the buttons (other than B) on a MegaDrive pad for CD32 games or games that need a CD32 pad. I don't know if this would fix the problem with the C button activating all CD32 buttons at the same time (as they do without modification), but it certainly wouldn't act as a Blue button. It would still work as a 2-button controller for all games that use those, and it would now let you use the A and Start buttons in Hired Guns and Flashback. In ADoom, all the buttons will work.
However... I don't think it's important that our modified controllers now allow you to do something that you can do with the keyboard anyway in a single game. It's cool, but it's not necessarily useful when it comes to using these controllers for all other Amiga games.
So what I propose for the ultimate Sega 6-button pad modification, to please as many people as possible, is to add this functionality so Hired Guns, Flashback and ADoom can use buttons A, B, C, and Start, but we map the UP direction to the X button, and turn Y and Z into turbofire versions of B and C. This would still let you strafe, fire, and open doors in ADoom, which are the important controls. But for all other Amiga games, especially platform games and racing games we would have a jump/accelerate button on X, which isn't uncomfortable to use with B and C, and we'd have useful rapidfire above the two regular firebuttons. Button A and Start (and Mode if you have a different brand of Sega 6 button pad than the DealExtreme one) wouldn't function for anything in any games except Hired Guns, Flashback and ADoom, or any game that's programmed from now on to take advantage of a modified Sega pad. The source code on how to read the pads is available with ADoom, so I'd recommend anyone still writing games for Amiga to add this functionality to their games.
Adding turbofire to buttons Y and Z might be tricky, but not impossible. There are instructions on adding a rapid fire circuit in a few Amiga magazines, and on Aminet here
http://aminet.net/package/docs/hard/autofire but I don't know how to follow that myself. I'm going to have a go at it anyway, but if someone who has actually soldered something before (unlike me) wants to have a go and take some photos and write up their results, I'm sure we'd all appreciate it.
