They have all gotten to where they are quite differently, and at different rates of growth over time. There are alot of similarities that can be explained by the fact that they are all about the same population sizes; it's the differences beyond that which I think we need to pay attention to, rather than the similarities, or the pros/cons of any one in particular.
For example, bad timing is quite relative here. Hamilton was amalgamated under Harris, as was Toronto and Ottawa. But KWC do not have to think about the rural townships. London, Hamilton and Toronto have built highways/manage regional travel in ways the province has provided for elsewhere. GRT massively benefitted from the temp student influx much as Brampton Transit did. The list goes on.
The agencies will recover, and if 'Line 10' and the Hamilton LRT are delivered, we may be having a very different conversation in 5 years about who's the best at what.
Hamilton was surpassing KW until probably 10 or so years ago where KW clearly came out ahead.
The thing with KW is that it's success has come from four major things to my eye:
1) Two major schools in the urban area (Hamilton has Mohawk, but I don't think it's the same as Conestoga because it's not in the urban area, more suburban, and Hamilton hasn't leveraged Mohawk the same way KW has Conestoga. Similarly, Hamilton treats McMaster as some weird sibling that everyone has to put up with at holiday dinners that thinks they're better than everyone else (which I don't think is true by the way). KW embraces being a university town.
2) KW embracing urban design guidelines that mean the urban area is actually nice. Hamilton hates downtown. Council meetings are often a discussion that goes "what about the wealthy Ancasterites??? Nobody thinks about them when we talk about downtown!"
3) Hamilton has underfunded and mismanaged it's municipal finances in a way that KW appears not to have (though I'm not an expert in KW finances Hamilton is a disaster).
4) KW was able to use its schools to attract big firms and employers offering urban situated well paying jobs, while Hamilton struggles to do the same with its health-care and other school focused sectors.
Despite this, Hamilton has seen a ton of medium to high quality development that KW hasn't seen. And I suspect when LRT starts this will be supercharged as developers eye up prime medium to high density zoned property along the LRT corridor. When it appeared LRT was about to start, many developers were using LRT to sell their units, but that slowed somewhat following the clear evidence LRT wouldn't be starting soon.
Hamilton lost out on thousands of new units simply because it didn't start LRT during the housing boom. It will still be better once it's started though. It's why LRT is so important to Hamilton. It's not just a transit project (though it should be focused on as transit) but it will be a total culture change to how the city identifies itself. With an downtown urban area double or triple the size of KW, with an LRT it will likely surpass KW as the secondary urban centre of choice. The only thing missing is a few larger firms/employers downtown.
I intend to vote for Loomis in the upcoming Mayoral election, partly because I'd like someone focused on business to attract an employer here. I don't expect much because politicians often have less power than they like to lead on, but I would expect Loomis to attract a business or two over Horwath, who has done very little during her Term.
That being said, I do hope KW continues to improve. I don't like to think of this as a competition, but opportunity. More mid-sized cities mean more choices and opportunities for Canadians and ultimately a stronger economy and more stable one. If Canadians can choose a secondary city with many amenities as the larger one while also being cheaper and quieter, I think that's a good thing. I like to try to visit KW once a year just to check out the progress.