Indeed, I wouldn't suggest retiring the diesel trains sooner than they approach their scheduled EOL.
And indeed, not that many suitable branches, but quite a few outer-end sections that may not be equipped with catenary in Phase 1, either because of the CN / CP objections or just because of the cost. In such cases, dual-power trains can help. Catenary to Bramalea, then using battery to Kitchener. Catenary to Markham Stn, then using battery to Lincolnville. Catenary to Langstaff, then using battery to Bloomington. And, of course the Hamilton GO as you mentioned.