It's gotta be said that lining up all of the main game chapters (RB, GSC, RS, DP, BW, XY) it becomes really hard to pick them. RB suffers from it being the first go and I feel it fumbles in some places. GSC has that horrible section where Crystal takes over and I find that Crystal is very uninteresting by herself and only works with Gold or Silver. RS is freaking awesome, Ruby and Sapphire are the best and some of the scenes are phenomenal. DP is also great but it's brought down because I feel there is some obvious favoritism towards Dia and though Dia is my boy Pearl and Platinum got robbed (especially in Platinum's case when it comes to the Platinum chapter). I honestly can't speak for XY because I have yet to read XY and I am waiting for the proper volume releases (which looks like it'll be ages from now lol since we still have to get through BW2 and the first volume of that hasn't even released yet), but I do try to keep up with the magazine releases and X seems pretty cool and so does Y so they might get a bump in my book eventually. I also feel the third version/sequel/remake chapters fumble far too much in places to end up high in my list but I get it, as a writer myself I see the conundrum in getting those games in chapter format when most of them are just the same games again. Of course chapters like FRLG are still pretty standout and Gold's reveal in Emerald is still awesome.
I have to go with BW though I flip flop between GSC and RS. Black is such a great character. He's a play on pretty much every shonen trope. He's the chosen hero of truth, but not before getting angry at the people who decided that for him and he even admits he has no idea what he's doing at many points towards the end of BW. He isn't the victim of fate or because the prophecy says so, but because he wants to fill that part. His team I feel is one of the more fleshed out of the bunch and Emboar never really stole the spotlight from the others. White is good also because instead of turning her into the action girl destined to be sidelined in the end like most female dexholders she goes through an arc where she gets stronger BUT she's still treated as more of a support, which makes sense. White was never destined to be on the front lines and I rather she be this than forced to be a fighter and inevitably job due to Black (looking at you Y). Not to mention I feel Black and White have a great relationship and the scene at the end of the chapter, you know, THAT scene really hits you in the feels. Also, I feel it has a very good transition to BW2 through the last few chapters. Both dexholders appear at the end, Keldeo and Genesect are put in place, Colress is revealed, and Team Plasma are clearly not dealt with. It's just the best transition between chapters to me. Crap I didn't even mention the dynamic between Black, white, and N. Great stuff.
So BW, that's my answer for the best. But again, it's a very close call and the answer changes daily lol.
To right the countless wrongs of our day, we shine this light of true redemption, that this place may become as paradise. What a wonderful world such would be...