This business is never going to be a hyper-profitable one for local stores.
MTGO's same-as-retail pricing isn't the problem- it's their refusal to actually invest resources at all levels (software, management, etc.) that is.
Both ideals are born from a pre-Amazon/SCG and Heathstone/online gaming saturated world. Forcing an artificial layer of scarcity is wholly unnecessary, as we've seen with the successes of Modern Masters. The game is popular enough that adding faux scarcity through restricted printings isn't something that is a boon to stores, players or their bottom line. It benefits nobody, but since it's The Way Things Have Been Done, it'll continue to roll.
They're not a bad company, but they're seemingly unable to handle their periods of success. Listen to MaRo and he talks about the cycles of Magic's popularity waxing and waning and the lifespan of players that come in and out of the game. He talks about these things like they're due to the moon's gravitational pull and just a part of the natural order of things.
They haven't really connected those cycles with their own practices. Stuff like the failing to meet basic expectations. Being too slow to adjust to secondary market pricing that allow external companies to exert pressure on their cultivated community. Not paying attention to MTGO's stagnation while saying things like "Hearthstone isn't our competition." And yes, forcing scarcity with their new products, forcing resellers like SCG to take advantage of what is ostensibly WotCs client is what drives people away.
The game brings them back. But imagine a world where they didn't leave in the first place. The money and goodwill they're almost literally throwing away is staggering.