Sugar (positives)
-The world design invoking urban fantasy and Earthbound overtones was really cool.
-The seasonal changes were also very cool, even if I have a bad habit of only playing this in the "winter" months.
-I actually liked the limited Pokedex because it created challenge and gave focus to the new 'mons.
-Can't deny that the Plasma takeover of the Pokemon League and everything that followed it was truly one of the best "final fight" scenarios in Pokemon.
-Ghetsis is truly an amazing villain, even if Gamefreak keeps toning down his implied atrocities.
-Bianca's storyline was very sweet.
-Decreased focus on HM's for travel and roadblocks. However...
-Infinite TM's!
-Made it easy to keep a team of 6 trained up without getting overpowered and almost without grinding.
-Final boss was actually a decent challenge (if not a fair one Mr. underleveled Hydreigon)
-It's a pretty good gateway game for new players, and works pretty well as a stand-alone too.
Beef (negatives)
-Cheren was soooo bland and underwhelming as the rival. N is arguably the real rival.
-The post-game level jump is huge.
-Stupid roadblocks (bridge is down, men dancing for no reason, etc.) This ties into my final point at the bottom.
-Beyond the joy of putting top hats and bowties on everything, Pokemon Musicals were really dumb.
-Some characters were under utilized, especially Concordia and Anthea. The Sages and Shadow Triad too, but B2W2 tried to fix that.
-The story is set-up as exploring the ethics of capturing, raising, and fighting pokemon, but in reality it was never about it at all. It was always about forcing your views on to other people, and in that regard it did tell a pretty compelling story. But if you do go in expecting conclusion or true debate on the ethics of cock-fighting, then you are left really disappointed and the "Team Plasma was lying?!" comes across as a really cheap cop-out to avoid giving it much thought. On TvTropes, this is called "Debate and Switch" or a work of fiction that sets up a moral dilemma or other painful choice, then finds a way to resolve it without addressing the issue it raised. I would have been fine with the "forcing viewpoints" plot if they were upfront with it from the beginning, but disguising it as a poke-ethics plots soured me. I really thought there would be a very deep story there, but they just jumped ship at the halfway point (or even earlier, depending on how you view the "kick the Munna!" scene).
-BUT ALL THAT COULD HAVE BEEN FINE if they hadn't sacrificed exploration for sake of story. One of my personal joys in the Kanto and Johto games is doing things out of order just because I could. Want to go from Lavender Town straight to Sliph Co. to finish the Team Rocket story, or do you want to go to Fuchsia get surf and then beat Giovanni an Articuno just for kicks? While this problem isn't unique to Unova (Sinnoh was just as bad, if not worse), Unova was definitely the most blatant and "in your face" about directing the player here and there just to get you to the next cutscene when the game wanted you to. I don't want to hear kids spitting empty platitudes at me every time a leave town, I want to discover hidden caves and secrets! I'll get to the story when I want to! And exploration was ALWAYS meant to be one of the big aspects of pokemon, and I felt that Black and White dropped the ball on this so they could focus on story instead.
I'm not saying that Pokemon can't have deep stories, Sea Mauville proved that exploration and story can go hand in hand. But I will say that I didn't like how Unova paced there's, and that's my biggest beef with it. The story pacing.