My choice: FireRed (BPRE)
Advantages:
- Comparing to R/S/E, it has much better graphics,
- Comparing to R/S, it has improved music and very nice tracks on Sevii Islands,
- Comparing to E, it is more stable,
- Comparing to R/S/E, it has nice text colors both for male and female sprites,
- Comparing to R/S/E, the intro can be done very well if you know how to make advanced scripts (because not everyone likes saving Prof. Birch)
- Comparing to R/S (and partly E), it has nicer font.
Disadvantages:
- Comparing to R/S/E, it lacks Realtime Clock (which can be useful if you want Day/Night to be implemented)
- Comparing to R/S, it is a little bit less supported by some tools (although it's not completely true)
- Comparing to R/S/E, it's harder to edit hero backsprites and edit intro sprites (which aren't present in R/S/E, there are battle sprites used instead. Only exception is Prof. Birch),
- Comparing to R/S/E, it lacks a good trainer device like PokéNAV,
- Comparing to R/S/E, it's harder to edit the world map
I would still recommend it, even if it has disadvantages, because if you use it as a base, you can produce really high quality hacks, rijonAdventures is perfect example. Or ShinyGold.
EDIT: Hope we didn't bump the thread.