Originals:
#1 BW/BW2
#2 RSE
#3 GSC
#4 XY
#5 D/P/Pt
#6 RBY
Remakes
#1 ORAS
#2 HGSS
#3 FRLG
Gen 5 is totally underrated. I love the exclusivity of the original BW games, limiting other pokemon from other gens until the post-game. A well-crafted and tight reboot. Of all the games it seems the most perfected.
Gen 3 is by far the most original of the regions. Thus its polarization, but I prefer regions that are unique and distinct, rather than blending in with the crowd. The pokemon feel exotic and really paired well with the unique environment.
Gen 2 feels like the original remake of gen 1. It's just better in every way! Graphically, it's my favorite game. The colored sprites have the most character of any gen. If only it was a bit more distinct from gen one and had a greater variety of new pokemon. Regardless, this is probably the easiest of the games to get into, not to mention 16 badges!
Gen 6 felt less distinct, including too many pokemon from previous gens, though mega evolutions are a great concept, the execution for many of them was abysmal. That said, the overworld, customization, new pokemon, fairy types, among other new features make i an AMAZING region!
Gen 4 had excellent new pokemon (barring many of the evolutions for previous generations), though the over-world wasn't inviting.
Gen 1 is boring and boxy as far as the overworld, though I appreciate it as the foundation to the excellent games which succeeded it.