unpopular opinion here, but I firmly believe there's never really been a good Pokemon story. I truly do not know what people are talking about when they mention the story in Gen V. When I talk about which generations or games I like I'm not talking about the story because they're forgettable and overall bad.
The biggest thing for me in a new game are the Pokemon designs and I think Gen V gave us some of the worst designs. There were also few characters I enjoyed. Also I see Gen V as the beginning of terrible Champions (ignoring Wallace). Alder and Iris are very bland and not exciting to face. I have really tried to approach bw with an open mind, but I cannot get myself to like it. Now bw2 I will give credit. I enjoyed the added areas, the addition of prior Pokemon, there are actually things to do in the post game, plus some enjoyable characters. I will say this gen has my favorite elite four.
Gen VI has really good designs imo, I enjoyed the addition of the fairy type, and trainer customization. Also the addition of wonder trade and the whole set up of the gts was perfect. Unfortunately xy was way too easy and Diantha was a bland ass champion. Also the post game was insulting. This gen has the Hoenn remakes which makes it a bit unfair to compare. I will say the removal of trainer customization was bull and the addition of the delta episode was so unnecessary. I really did not need Pokemon to add dimensions to try and explain things that didn't need explaining to begin with. It's Pokemon, it's not that deep. Lastly they cut the Pokemon Frontier. The thing that I was most looking forward to from the remakes wasn't in it...
It's hard to say which is better for me at this point because I have major gripes with both. If you want somewhat of a challenge gen V is better. If you care more about design gen VI is better.