"I also am big on doing family trees, and I can't imagine how much more difficult that would be if people had different last names throughout my families history."
My family came over in like 1902 or so, and some of us got Ellis Islanded, and others didn't. So my very immediate family have a rather ethnic, hard to pronounce, hard to spell last name, but there are cousins out there with 2 different anglicizations, one of which doesn't even remotely look like the original name. Just saying
I took my husbands last name largely because my maiden name was long, hard to pronounce, and even harder to spell (and some family issues, and because I'd rather not be googleable), and our children will share that last name. However, I can promise you that anything that even remotely resembles the last name counts, legally. So if you wanted your children to have the last name Smith but they decide later to hyphenate to, say, Smith-Johnson, that works too, without dealing with legal changes (my niece is doing this; her parents weren't married, her legal name is the mom's last name but the dad's is added socially, and effectively legal for stuff like school documents).
I think having a different last name across a nuclear family can be a pain in the butt, but it will probably be less so as time goes on because blended families are more common. In my own situation my parents were married, I had my dad's last name/mom's married name (M), they got divorced, mom never changed her name back (L) but had a kid with another guy who has his last name (J). There was a chance that there'd be 3 different last names in my 3 person immediate family. The most that happened was that school and my little sister's friends would default to calling my mother Mrs. J when she was really Ms. M. There was never any confusion as to who the parent was, never any legal hassles, etc. Heck, I even have a friend whose mother socially changed her name entirely, adding a letter to her first name and changing the pronunciation, and picking a different variant of her last name. From what I know, that wasn't really a big deal, though there'd be double takes when she'd answer to the other name in class rosters.