The biggest problems with OW have nothing to do with a specific route or region. Their problems lie at their core thinking, and its complacency, lack of aggression, and non-proactive thinking.
The JAL drama was a result of typical AA/BA complacency, and allowed DL to lay siege to a corner of the OW castle.
The "African Gap" is a prime example of their lack of aggression, and has allowed DL/Skyteam to make big inroads in the continent. I've never understood why BA/OW can't replicate the Comair model in Ghana and/or Kenya. Then there's AA's failure to take advantage of MIA as one of a the best locations for an African gateway in the US.
I would also point to LATAM, as a lack of proactive thinking. Any time a large percentage of an alliance member goes to market, red flags need to go up. As things stand now, LATAM could go either way as far as alliances. If OW were ahead of the game, they would have collaborated(within the law) to buy the shares of LA that were for sale previously to ensure more a greater chance of LA staying in OW.
If you fixed the first three problems mentioned, I'm sure we would see a much stronger and dominant alliance.