The biggest upside to codeshares for customers is that connections on partner airlines can be purchased on one ticket, providing protection in the case of a misconnect.

One of the downsides is that there is sometimes very limited availability on the codeshare. A few years ago I tried buying YHZ-YYZ-BRU with the second leg operated by SN. This was 6 months out, but AC didn't have the inventory to sell me 5 tickets - either on the website or talking to a phone agent. There was availability on the SN site but prices were much higher.

Another downside is that you can't use discount codes.

For single segment tickets, there is even less upside.