So many questions... like, should passengers on the Wigan - Atherton - Victoria trains be inconvenienced by having the service terminate at Salford Crescent so that passengers can change to a bigger train there?
Should we reduce Northampton's train service to a Rugby - Milton Keynes shuttle, so that Northampton passengers had to change to a bigger train there?
Or is this just about messing bus passengers about?
It's not about messing anybody about. Using each mode for what it's good at provides a faster end to end journey and makes a more effective use of funding.
The Atherton Line example isn't a very good one, because the Atherton Line is precisely one of the "rapid transit rail" routes that would form the basis of the network. The Northampton one is poor as well, because the thing is you can run a train from Northampton to MKC then fast to London at 110mph (the difference between 110 and 125 is only a couple of minutes), whereas a bus in a city is stuck to running at 30mph with frequent stops (generally, cycling is faster than city bus travel on a good many routes). Or are you proposing an express bus service from Alty to Manchester via the motorway?
Actually, it's worth noting this regarding the south WCML example - some people
actually do take Avanti to MKC then change, though the timetable doesn't make it that easy. But if you take a look at connections that
are easy, people do use them. Pre COVID, somewhere around 30 passengers take the 1816 Euston-Leighton-MKC-Northampton-wherever, and change at Leighton Buzzard for a one-stop journey to Bletchley. They do this because it saves them about 10 minutes over the direct, slower service. The fare is the same, the change is easy (same platform and pretty much can't be otherwise), the connection is reliable (because the slower train is held at Ledburn for the faster one to pass, because if it wasn't it would cause too much disruption). So people do it. I'm informed that despite most likely having to stand it's quite common for people to do similar southbound in the morning too.
Of course one model you
can use is something like the Leigh or Cambridgeshire busway, where you have local buses wandering around local places then coming together to run fast into the city on a dedicated, congestion-free corridor. That is a workable alternative concept, but the thing is, it
isn't the concept that applies to most Manchester city bus operations, nor, unless you close the railway or tramway and convert it to a busway, will it do. Just putting in bus lanes isn't enough, as the road still has a 30 (or sometimes even 20) limit on it, 40 at absolute best.
It's not a case of English Exceptionalism, it's more a case of "fine if it works elsewhere, but we're not starting with a blank sheet of paper".
It all sounds very nice and Sim City in theory but we need to come up with any new solution mindful of the disruption that would happen if we moved from where we currently are to where you want to be.
Which might necessitate phasing the changes and coupling them to things like rail improvements, not just doing them on "R-day" (aping "D-day for deregulation

). It might for example not work so well if you start shuttling people from Partington to Flixton/Urmston (as I mentioned above) for a sub-hourly 2-car 1980s DMU local service to Manchester. But let's say Northern Powerhouse Rail is built, and so the CLC loses its long distance purpose, and so we end up with a 15 minute frequency (or better) stopping local service on the Manchester end of it (let's not debate if that's a 25kV EMU or a tram, it doesn't matter for the purpose of this thread). Rail usage would increase, and a shorter journey would be available by connecting to it. So then it makes sense.
For example, under the status quo, pensioners can get a direct bus from their house into the city centre
If they live actually on the A57.
Under my understanding of this proposed model (?), the bus service to the city centre would be scrapped and they'd have to walk a longer distance to a tram stop (bearing in mind that tram stops are much further apart than bus stops) and then pay for the tram fare (since these aren't free right now, I'm presuming that the same fares would still apply on trams in this proposed model?).
They could use a local shuttle bus. Indeed, that sort of service would be more financially feasible to operate because you wouldn't be wasting the buses shoving them up the A57 about 150 metres away from the railway.
No, the same fares wouldn't apply in the proposed model, and indeed in most of the PTE areas travel on all modes is free to passholders. TfGM has imposed a small annual charge for this, but it really is a small charge; personally I'd favour upping Council Tax and removing that charge as it's unfair and regressive.
Or maybe they'd be lucky to live on a bit of road where there was still a bus service to the nearest tram stop, where they could change modes of transport? But I can't see how feasible those bus services are going to be if they are just running to the closest tram stop and back.
The answer is that they don't have to be financially viable in and of themselves, because the viability is considered over the whole
system. That individual bus might lose money, but that's the wrong way to think about it - this is the most beneficial change that regulation of this kind can provide.
What about people who can afford the bus fare into town but not the (higher) tram/train fare? They now have to pay more at the same time as having to change modes of transport?
You deal with affordability by way of various kinds of means-tested discounts, not by differential fares.
And, since we aren't starting from a blank sheet of paper, where are the additional seats on trams for all of these bus passengers (who are no longer bus passengers, because their bus service has been scrapped to force them onto trams)?
They are wherever Metrolink's trams are manufactured, if more are needed. Again your argument is flawed; if tram use increases, you increase the length and number of the trams. You wouldn't go "oh, we aren't buying more trams, we'll put a bus route on instead", that would be plain silly. There is the counterexample of London, but the Tube is in most places physically full, Metrolink is not; most trams operate single most of the time, and so doubling capacity is simply a case of buying more trams and a bit of depot land.
How close to the city centre is a bus route allowed to get without getting scrapped? I know the way that the PTE forced people from south of the Tyne to lose their direct bus into Newcastle so that they'd change onto the Metro for a one-stop journey across the river. So would all Trafford services have to terminate around Cornbrook for passengers to fight their way onto a busy tram? Do Middleton passengers find their bus into the heart of the city now stops around Queens Road, where you're expected to get off and wait for a tram?
I mentioned above that the Gateshead example is flawed, and like it so are all of the others you have applied here.
Where you have a corridor that is basically unserved by rail, it doesn't make sense to mandate a connection just short of the city centre. Clearly those services need to run through, and they typically do in Germany, too. You'll note I didn't propose rerouting the Wilmslow Road corridor buses to "S-Longsight" or something, because that would just be silly. Of course, Wilmslow Road needs a street tramway whacking down it, but given that there isn't one and isn't likely to be one, so we are left with long distance bus. Bury is actually very similar to the Liverpool 310 argument I used earlier - the bus isn't there to compete with the tram, it's there because that end of the (fairly populated) A56 runs quite a long way away from the tram route for all but about 2-3km of its length, and the corridor is relatively linear so there aren't obvious circular or figure-8 local bus connection routes.
It makes sense to consider this where either you've got a rail service very close by (the A56 is a good example), plus further out where the model will be a short local journey on a standee bus to get to the nearest railway station for a faster trunk journey. This is the model you will see around the world. German cities do have buses penetrating their city centre from close-in suburbs that don't have rail, and so would we. There is no hard and fast rule, but that's the basic idea.
To use a few more examples - Rochdale is a distinct town, and so a local bus network feeding the railway station with an improved local EMU service makes sense to move towards. (The tram is a nice example of the above, actually - it isn't intended to provide for Rochdale-Manchester journeys even if some might use it as such). There's also an obvious fig-8 local route around Castleton station. Oldham is broadly similar, and the tram route runs about 100-200m from the A62 near throughout, though there are a few long gaps where additional stations might be beneficial before you did lop the bus service down. And if you move round a bit, the A662 has a tram line running down it, so that's not a place to run buses to compete with them. But there is literally no point having people from Openshaw and Beswick shuttled to a tram stop to connect into Manchester, because that would be far slower than taking them all the way in by bus.
The arguments against this idea tend to be the cases where it's been got wrong in the UK, not where it's been got right, either in the UK or elsewhere.
Maybe if you had hundreds of millions of pounds to build all the new tram lines required to accommodate all of these people, I'd agree. If this was some GMPTE/TfN masterplan for 2050 then I might admire the Blue Sky Thinking (whilst acknowledging that there was little likelihood of it ever coming to pass). Maybe if we were building a brand new city, sure, copy the best integrated system that you can find. But we're not in that position, we're starting from here, things are as they are, so all the abstract thinking needs to be grounded in the reality of how existing passengers on existing services would be treated.
And the first step is to regulate, so we can then do that long-term planning without Firstarrivacoach mucking it up by competing with it. It doesn't have to be a big bang, it can indeed be a 30 year plan. But the first step is to do the ones we can do because the rail capacity is there, and then we move on to improve the system as we go along to provide a more effective public transport service for the whole city, not just for those who are fortunate enough to live directly opposite a bus stop on the 42 or 192, or a railway station or tramstop.
What if it is an abject failure after, say, 5 years? (I don't believe for a minute it will be, but what if it was?) - just deregulate again. We did it once, it can be done again.