For me, I think using SMDs is probably easier overall. Maybe it's because the soldering isn't a big issue? (That's what lunch breaks at work are for.

)
When I etch my own PCBs, I
try to keep it 1-sided and not have to worry about screwing up the alignment. (I just add a couple jumper wires, where I can't get around crossing 'em.)
So, when I can use SMDs, it eliminates most of the drilling. And I really hate all the micro drilling!
And when you
have to go 2-sided, there are no sleeves in the vias, either.
So, you end up doing twice the soldering, with thru-hole, to tie the top and bottom annular rings.
Maybe I should get out of the PCB making game and just let a board house do it?!

I'm curious, who did you use to fab it? And did you get stuck with a big setup fee, for the small run? And if it's not too personal....how much?