I would like to see the flagship have some difference between the other cap ships besides getting to start out at a higher level than its brethren, whether it be the flagship is bigger, has a different icon, paint job, "aura" of some sort.
I also think that eet has a point. In WC3, there was a "starting Hero" mode and I do think that is comparable to our flagships now. Whether the devs want to deviate from this simple game option or not is up to them, but making the flagship different in some way would be pretty cool.
