We have cleared into and out of Utila in the past year, and out of Roatan.
Roatan is expensive and difficult. It will probably take you two days to get everything done if you can track down the port captain
and get the immigration officer to even give you the time of day. The offices are not near any cruiser anchorage, so you will be taking taxis or buses to get there. The buses do not run straight there, so you will be making non-intuitive transfers.
Utila is a cakewalk. You go to the port captain
and immigration - which are side by side offices right in town by the harbor, pay some very small amount ($5?) and you are done.
Guanaja is likewise a cakewalk, if you want to check out there, or are coming from that direction.
It is possible that this has all changed in the past year, since we have been gone for 9 months or so.