Thing is that MM (for a whole variety of reasons, some of them nothing to do with his abilities) has never been a good Speaker. He probably was a poor choice to start with, as he was not supported by the leadership (always going to make things more difficult) and not felt to be non-partisan. So a bit of an upward struggle there. Then he does appear to be a bit of a bully, ready to blame others when things have gone wrong (eg the police involved int he Damian Green affair both say that the official they dealt with spoke on the phone to MM when they were there, and yet he has claimed it was entirely her fault they were allowed in).
Then the Fees Office was under his control. The rules set for it were clearly too vague, and accounting was far too club like (but then the HoC has operated like a gentleman's club for many many years) but there were calls for reform, and the rules set in 2005 clearly say that expenses will be subject to FOI. He fought them tooth and nail, even pressing on with appeals when his own lawyers told him not to. OK so the senior officials might also have been keen on secrecy (I bet they were), but he was their boss, so no way did they act on their own (they would have had to have his OK for the legal bills alone).
And don't lets forget that they have still not complied with the FOI request, even backed up by the High Court. We only know (certainly in such salacious detail) because someone leaked the information to the Telegraph, and his response to the leak - get the police on to it.
I feel no pity for him at all, indeed he should have resigned earlier instead of waiting until he was pretty much evicted.
I do agree that there is a lot more house clearing to be done, but I really think the parties would be committing electoral suicide if they don't take some pretty decisive action.