Does your starting city affect anything?

[Taika]

A couple early MSQs, and taxes on items sold on the market board would be about all I think?

You can hire retainers from other cities than your starting city, so it doesn't really affect that.

[ZhaneX]

You can hire retainers from other cities than your starting city, so it doesn't really affect that.

True, but given that you'll get the initial quest in your starting city, and thus hire your first retainer there, and then probably second out of habit...
Of course, maybe that's just me being habitual and/or lazy.

[Niwashi]

You can hire retainers from other cities than your starting city, so it doesn't really affect that.

True, but given that you'll get the initial quest in your starting city, and thus hire your first retainer there, and then probably second out of habit...

The quest that unlocks retainers is in Waking Sands for everyone. It doesn't correlate to your starting city. (Besides, even if you did hire your retainers in the same place, you can still change which city they're selling from at any time. I spread mine out, so that I have one selling from each city's market.)

The actual differences are: 15 levels worth of the story. An occasional slight dialog change thereafter. And one gear item that's unique in name, but generic in appearance. The only part of that that's significant is the first 15 levels of quests. (I consider that part worth starting three characters, one from each city, and playing each of them through that first segment of the storyline, up until the point where the stories merge, even if you don't want to continue with all of them after that. People who aren't as interested in the storyline probably wouldn't, though.)