It seems to me that the trouble is with B&W rules.. not with the MD-on format.
QFT. The MD-on format may have been a little out of hand with the broken SPs but they were easily combat-table.
The BW rules are what are messing the game up. We thought that with a HGSS-on rotation, the BW rules wouldn't be bad. Nerfed Candy? That will slow down the format SO much. Yep, it sure did, but with Catcher, Plus Power, Junk Arm and Tyrogue in the format with T/S/S first... that's what's making most games have a flip for the game.
Ok, Tyrogue can't beat Reshiram/Zekrom starts but we have to remember the majority of the meta is basics that are donkable by Tyrogue.
In this format, evoling first is very big. In last, it wasn't that important. Even racing to see who could level up Chomp C X first wasn't that big of a deal since there were so many counters available at the time. Draggy and Ambipom helped this. Not to mention whoever when first had advantages and disadvantages and same for 2nd.
IMO, the last format was quite balanced.
You can say that Luxray was really bad for the format not allowing everything to set up and say the format was bad, but we also have Donphan who, when catcher is released can manage a T2 60 snipe. Just like Luxray.