You should also consider whether you want to hack Gen III like most people do, or if you want to go the Gen II route (like I mainly do) or the Gen I route. Gen I has actually been completely disassembled over on another forum, and people have been doing some really impressive things with Red Version lately. Just pointing out that there are other games than just R/S, E, and FrLg that also come with their own advantages and disadvantages.
I'll try to start a list here, but it will be very incomplete and just sort of a rough outline that anyone is free to add onto.
Ruby and Sapphire:
Pros:
- Secret bases
- Dive functionality built in
- More documentation than Emerald
- Mach Bike and Acro Bike functionality
- Contests
Cons:
- 1 town map
- Most information is outdated
- Probably more stuff that isn't coming to mind
Emerald:
Pros:
- Contains many of FireRed's improvements
- Secret bases
- Dive functionality built-in
- Mach Bike and Acro Bike functionality
- Contests
- Has placeholder location names for all of the areas in Fire Red, so you probably won't need to repoint the name list to add more (even though it isn't complicated to do that).
- Support for both RSE style (tall) door animations and FrLg style (short) door animations
Cons:
- Some tools don't properly support Emerald, because they based their support on outdated information
- 1 town map
- Less documentation than R/S or Fr
Fire Red:
Pros:
- Multiple town maps allowing multiple regions easily
- Tons of trainer image slots, as it contains the trainer sprites used in RSE as well for no apparent reason (these images can be used on their own, or replaced to easily add more trainer types)
- Widely supported and documented
- Support for both RSE style (tall) door animations and FrLg style (short) door animations
Cons:
- No Dive support built-in (can be added with scripts if you know what you're doing)
- No Secret Bases
- No Contests
- No Mach Bike or Acro Bike functionality
Gold:
Pros:
- Patches exist to add the Physical/Special Split, Fairy Type, and other useful things
- Widely supported by tools
- Crystal's expanded tileset system has been ported to Gold
- Contains 2 regions and 16 badges by default
- A fair amount of documentaion
- Real-Time Clock and Day/Night system built in
Cons:
- Limited colours and amount of tiles
- Some things there aren't editors for so you have to do them manually
- No gender selection (Although these days some of us have managed to add it anyway)
Crystal:
Pros:
- Has been partially disassembled, allowing a lot of things to be edited as plain text instead of in a hex editor and then recompiled into a working rom (and using labels instead of manually finding free space and pointers)
- Has gender selection
- More areas than Gold
- Battle Tower functionality
Cons:
- Must know z80 assembly to use the disassembly
- Outside the disassembly project, there is very very little documentation
- The disassembly is not labeled very well
- Limited colours and amount of tiles
- Some things haven't been disassembled yet so you still have to edit them manually
Red:
Pros:
- Has been fully disassembled. You can get a copy of the source code, edit anything you want and recompile it without worrying about pointers things.
Cons:
- As this was the first generation, it has more bugs and things that are coded awkwardly by default to work around
- No built in scripting language like all later generations have, all NPCs and other things are scripted with z80 assembly language like the rest of the rom. This makes it more difficult for beginners but much more flexible once you know what you are doing.
- Limited colours and amount of tiles
*Please remember that this list may not be 100% accurate, as I am tired and have not extensively hacked every rom that is commonly used as a base.
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