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You've clearly done some homework as your tentative itinery is logical for your time frame and the time of year.You can expect snow almost certainly in Cappadocia and possibly some in Istanbul too but the Aegean coast see's very little snow so that would be a good area to head to for for clement weather conditions in January.Although the Gallipoli peninsula can be rather chilly and wind blown but as I see you're from Oz then I'm sure that won't put you off :)A warm water proof jacket and boots will see you okay.
Flights from Kayseri to Izmir are covered by SunExpress and Pegasus Airlines but they don't fly every day so you need to check when they are for best times and prices.
Using Selçuk as a base you can of course visit Ephesus but also Priene,Miletus and Didyma-(local companies offer day tours to thoese 3) and visit Şirince village close to Selçuk.
A longer day out could be a day tour to Pamukkale too.If you prefer not to take that tour then you can go by bus or train yourselves,stay overnight there and then take the bus or train direct to Izmir.
Once there you could take a bus to Bergama which is a very interesting site to visit and would break up that rather long journey from Izmir up to Çanakkale if that would be better for you.Staying in Eceabat puts you very close to the ANZAC zone.
From Gallipoli it would probably be better to return to Istanbul via bus.You could take the bus to Bandırma and then the ferry over but in severe weather the ferries can be cancelled meaning you'd be stranded there!Well,not stranded but you'd then have to look for a bus going to Istanbul and hope there is one leaving soon.....
You could do all of this and still leave a good 5 or 6 clear days at the end for Istanbul.
BTW,at roughly the same time earlier this year forum member Resmen(another Aussie),also did a tour of about 3 weeks during our worst winter for 40 years!He visited several of the places on your list and wrote up an excellent trip review.I think it is the first one on the trip review sticky so that could be useful reading for you.
Hope this is a help.....

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Thanks very much Sarikanarya. This looks really helpful. Just one thing - visiting Gallipoli is only one idea we had. Any other options of interesting places to visit as we head back to Istanbul would be good to hear. We enjoy walking and love seeing interesting villages, coastline etc. The south sounds fantastic but we don't really have enough time, and from my reading it sounds as if the weather might not be great in January.
Thanks for taking the time to help.

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Hmmm,at this time of the year the northern Aegean area is sure to be iffy weather wise.Another option is to visit Ephesus and then go from Izmir south maybe down to Fethiye on the Med.coast,still no guarantees on the weather but sure to be milder.Around Fethiye there is plenty of interest to see including Kaya Köyü the Greek village that was abandoned in the population exchange.Fethiye also marks the start of the famous Lycian Way too.You could then fly back to Istanbul from nearby Dalaman airport,flights are very cheap and frequent.But this would mean leaving out Gallipoli though.

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Thanks, this option sounds interesting. I'll have to look at the flight times - maybe it would be better to fly into Dalaman and out of Izmir. Do you know how easy it is to get seats at that time? Will we be able to play it by ear, or would that be risky. As always, the weather is the big unknown so we were hoping not to be too committed. We have booked a hotel in Goreme for 3 nights (I think - must check that) but may want to stay longer as it sounds amazing! So much to see, so little time........

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Sarikanarya, you are a mine of information! Thank you for sharing. You have given me plenty of ideas to think about and to research. The translations for the flights site will be especially handy.
Thanks again.