I agree that what you have suggested should happen. However there are quite a few barriers to this. Whilst through train/tram fares are available, where there are alternate routes between the same places train and tram ticket prices are inconsistant and inconsistant. For example between Altrincham/Navigation Rd and Manchester, it is generally cheaper on the train, and you are unable to travel one way by train and the other way by tram on a return ticket. To allow this the prices would have to be the same meaning either train prices would have to rise or tram prices would have to fall. TFGM are unlikely to be able to afford to lose revenue with lower prices so it would be more likely train fares would rise to match tram fares. This then would cause inconsistancies with other fares across GM as most fares within GM are set in price bands. There would also be further inconsistancies as with the opening of phases 3a/3b there will also be new Metrolink/NR interchanges at Ashton, East Didsbury, Manchester Airport and Rochdale as well the existing one at Eccles.
There are also inconsistancies with the current Metrolink zones. When the system opened zones were banded A-G. Zone D was the city centre and then there were 3 stations in each zone outside the city regardless of where geographically the stop was. That means a journey from Bury to Whitefield costs less than a journey from Altrincham to Sale despite it being a longer distance. Now the system is becoming more complex the fares structure should be revised
The only way round this would be to totally change rail and fares in Manchester. Now would be a good time for TFGM to work out how to do this as Northern Rail and TPE who set rail fares in GM have their franchises coming up for renewal and TFGM may be able to persuade the government to require the new franchisee to fit in with TFGMs plans and also require the new franchisee to supply new compatable ticket machines and card readers etc.
I would propose 5 zones which would broadly fit in with existing rail/Metrolink zones.
Zone 1: Central Manchester and Salford
Zone 2: City Fringe - Stops within 2 miles of Zone 1 including Old Trafford, Levenshulme, COMS, Chorlton, Broadway, Crumpsall, Gorton, Central Park
Zone 3: All other stations within the M60
Zone 4: Stations outside M60 but within 5 miles of it
Zone 5: Stations on outer fringe of GM area such as Littleborough, Bromley Cross and Wigan area.
Some stations could be in 2 zones similar to Greater London, for example Salford Crescent and New Islington could be in both Zone 1 & 2. Stations right by M60 such as Stockport, Besses o th Barn, Brinnington could be Zones 3 and 4.
Other zones could exist to stations outside GM in Cheshire/Derbyshire/Lancashire for Rail travel only e.g.
Zone 6: New Mills, Poynton, Alderley Edge, Knutsford, Birchwood, Adlington Lancs.
Zone 7: Edale, Congleton, Northwich, Warrington Ctl, Chorley, Blackburn
There may however be conflict with other PTE's if zones extended into Mersey/ W Yorks.
I think the biggest problem will be getting private rail operators to invest in the technology and agree fares.
Integrating bus travel is perhaps more difficult as services are operated on a commercial basis and TFGM have no powers to set fares. Bus operators have combined tickets under System One but single fares are often a lot more expensive than the equivelent train or tram fares, especially off peak. Unless the government change the law to allow regulation/franchising of bus services and TFGM to set fares, then London style intergration is a long way off.