He did his best with what he had. Albany screwed the MTA over, the Union and its members get pay raises screwing the MTA again. You have 2 groups pulling the legs of the MTA, I think Walder did an exceptional job trying to balance them. There is no way you can satisfy everybody in that sort of situation. The service cuts were inevitable really. Perhaps the money used to innovate the technology in the system could've been used to hold back the cuts or a fare hike, but I'm pretty sure it wasn't enough being that the countdown clocks were relatively inexpensive, and the new website job and advertising campaigns are merely specks of dust admist the whole financial crisis.
If you were Walder, you would probably take the offer for the MTR, run by a joint public/private corporation with government support, and a shitload of expansion projects. Sounds fun, being a visionary there without the fear of getting a bad image by politics and bureaucracy. I still think Walder should ride out this whole mess in the MTA, he started these projects, he should finish them.