First, in comparison to Ford, Miller was a God!
That said, he did do things I did not agree with. While the taxes he brought in were arguably necessary, I would have rather seen it that other municipalities could implement their own taxes as well, or at least make them region wide. That way one wouldn't simply have to live on the north side of Steeles to save themselves $60 per year on their vehicle registration. Also said money went straight into general revenue, rather than specifically into transit where it could do the most good.
Also he did very little to address TTC culture. Very slow adaption of smart cards and electronic payment, no investment in larger buses, two hour transfers left as a "pilot project" for 5 years on a single route without any oversight (and continue to this day), poor handling of customer complaints and concerns, etc.
Also he tended to focus too much on local matters rather than uniting mega city. For example, forgiving the Ford rhetoric, but Transit City's tight stop spacing really did make it look more like a fancy streetcar than true light rail rapid transit, which is what the suburbs need. And while bike lanes are great and I don't support removing them, some of the locations for them could have been better thought out.