As someone that has played every Pokemon game to date, and who hasn't watched the cartoon since the first year my sons got into it, I think that Emerald is still the best overall Pokemon game ever made, and what I have seen so far from BW I don't see my opinion changing at this time next year.
EVERY region has its good and bad points. EVERY region has bad Pokemon concepts. EVERY region has points in the story that make you scratch your head. From a conceptual perspective, nothing beats RBY. It laid the foundation of the property and while other games have built upon the original concepts it would take something major for a game to beat what RBY gave us. From a storyline concept, nothing comes close to GSC, and that is even including the halfassed Kanto addition that wasn't even improved upon in HGSS, which was highly disappointing and basically proved how GF has lost touch with the property. For functionality, nothing beats DPP with its Wi-Fi feature allowing someone in the US to battle against someone in Japan.
Now while RSE isn't the best at any of the aforementioned aspects, its drawbacks are also less than the drawbacks of the other games too. RBY had limited functionality (although FRLG did alleviate that somewhat), GSC really had bad conceptual designs (even though RSE tends to get a bad rap), and DPP has by far the worst storyline and even worse designs than GSC. RSE didn't have the best designs, but they certainly were innovative and provided the property with three really good starter Pokemon, along with some excellent typings. I was also quite disappointed when I found that RSE moved away from the Day/Night feature in GSC instead of expounding on it. That said, it provided us with a much better breeding and stat system, not to mention the terrific addition of natures, and the revamping of the Effort Values and held items. The storyline could have been better thought out, but the addition of Secret Bases and the Battle Frontier more than made up for it. If you didn't like Secret Bases, then you probably didn't realize the true potential of it as it pertains to breeding and competitive battling. It is by far one of the greatest additions ever to the property. I have set up over 20 different Secret Bases on my Emerald version that are filled with Pokemon that help me max out EV stats on a Pokemon in minutes rather than hours. Then the Battle Frontier AI is actually challenging when compared to the pathetically weak in-game AI. Lastly, while it doesn't have the true Wi-Fi capability that DPP has, in Emerald the addition of the wireless connector was a BIG step in that direction. Being able to trade and battle without being tied to a 3-foot tether was a great improvement.
Personally, there are A LOT more people I know that dislike the Sinnoh region Pokemon than the Hoenn region Pokemon, with myself included. I didn't like going from 7 to 10 Legendaries in Hoenn, but then you have Sinnoh that went to FOURTEEN! How many can we expect in BW? 18? 20? 30???? Still, when you compare Hoenn Pokemon to other regions, they really do hold up rather nicely and there are only a few what I would consider bad concepts.
