I have booked a ticket with a code-sharing airline in preference to the operating airline, which saved me about AUD200 (about 10%). Same flights, days, baggage, meals, etc. However, I wasn't able to check in online with either the ticketing airline or the operating airline and I was assigned a middle seat in a block of four, down the back of Y class on a (very) long haul flight, next to a chap with very broad shoulders. I didn't spot this restriction in the terms and conditions, and they might not have even been mentioned in them. This was despite being a frequent flyer member on the operating airline, with seat preferences always having been honoured when booking directly with that airline. My partner had a similar experience with a part-code share flight - on a different route and airline - where online check in wasn't available and a middle seat on the code-share flight had been automatically assigned.
I suspect that the code sharing airline is assigned specific seats on the flight, and to keep computer and business systems simple there isn't the same flexibility on seat selection and online check in. In my case it was a full flight with no chance of a seat reallocation. In my partner's case luck prevailed and a seat reallocation at the gate was forthcoming (after asking nicely!).
So in buying the cheaper option you might be giving up a degree of seat flexibility and comfort. In my case I learned a lesson and I now tend to spend the extra money and book directly with the operating airline, unless the savings really outweigh my tolerance for discomfort.