Apart from their schedule changes (and abandonment of the LGW-OPO route), my main criticism is that when things go wrong with GB, they go spectacularly wrong- delays can run into many hours (e.g. my last OPO flight was delayed from 1300 to past midnight). They clearly use their fleet to the full, with little contingency. I guess that's the price you pay for competitive fares.
On the plus side, their cabin service is good and seems consistently better than BA mainline (although of course it's a considerably smaller crew staff and therefore easier to maintain standards).
On the whole, I love them, rather than hate them and I think the savvy traveller will understand why things are like they are. On balance probably doesn't affect BA's reputation.....it's much more damaged by the stupid annual summer disruption.