I don't think there is much concrete, but here are some things that it effects.

1. Performance. You view almost everything via your instance. So picking one running with capable hardware and ideally close to you (network wise) will give you a better experience.
2. Reliability. If your instance goes down you are basically offline. This can be hard to predict for the future.
3. Trust. Your identity is "owned" by the instance. So if they wanted they can impersonate you. This can also be very hard to gauge.
4. Longevity. If your instance shuts down it will be quite inconvenient and your identity will be lost, so you may want to try to predict which instances are likely to last.

Content is actually not really on my list since you can subscribe to any communities from any instance. It is true that the instance can provide some content discovery purpose via the local and known communities page but I would argue that separate service which track communities across all instance are better for this purpose.