I think that the best way for Toronto improve its transit is increase the fees for non-Torontians, not just using road tolls, but through the TTC as well, which can be easily done once Presto is fully implemented.
For example, if the fare for residents of Toronto is $2.50, then the fare for North York, Scarborough, Etobicoke, York, and East York residents should be $4.00, while those living in 905 should pay $5.50 to use the TTC. These fares would more accurately reflect the extra burden that suburbanites place on TTC. Once they pay their fair share for the service they use, it will help ease the TTC financial woes, and maybe even help pay for TTC expansion as well.
A unified regional zone fare system would do that exact same thing, without being so politically toxic. If most 905ers are bound for downtown, there would be little difference in a unified fare system vs an 'outsider tax' on people using the TTC.
It's under my system map, but you can see the fare zone system I'd like to see here:
https://dl.dropboxusercontent.com/u/43869799/GTA System Map - To Scale_small.jpg
As you can see, Toronto from the Lake to the Humber to the 401 to Vic Park would be Zone 1, with a base fare of $2.50. Zone 2NW would be from the Humber to Hurontario, up to the 407 and then 7, then back to the 407 to Yonge. Zone 2NE would be from Yonge, along the 407 to the Toronto-Durham line, down to the lake. This would be an extra $1 for local rapid transit (BRT, LRT, or subway), or an extra $1.50 for express rapid transit (GO REX, GO, express BRT routes like the 407 Transitway). The fare zones radiate out from there, with a total of 5 zone rings, for a maximum fare of $8.50 using express rapid transit (unless you're travelling from the Rural zones, in which case the fare is route-dependent).
My point is that there are other ways of ensuring that people pay for the length they travel, instead of just slapping a surcharge on anyone coming in from north of Steeles, west of the 427, or east of the Rouge.
$2.50 base fare and unlimited travel on local transit, $1 for each additional zone via local rapid transit, $1.50 for each additional zone via express rapid transit. Simple, easy to figure out, and I think much easier to swallow politically than making it a 416 vs 905 issue.