I guess it matters in some specific scenarios unless it is easy to migrate your profile from one instance to another.
The scenarios I think about are:
Geolocation. I guess the closer the instance is to you, the faster the content will load. So the closer the instance, the better.
Geolocation "blocking". I guess if a instance is in one country and that country's legal system mandates the instance to be blocked, you will lose access to the "fediverse". So, I guess, the more likely the instance is to blocked, the worse.
Defederation. If for some reason your instance gets "disconnected" from the others, you lose access to the other instances' content. So I guess "reputation" is key here.
Uptime. Not all instances stay up the same, I guess...
Instance backend versions. Some clients only connect to specific versions.
But, honestly, even considering the above, I can't comfortably "choose" a instance. That's why I came here for help...