I have written a way to check the current version on updating and upgrade anything database related that I may need, but I don't think that would be the actual problem here. I also get issues with upgrading things - I couldn't upgrade to WP 3.5 without uploading my site manually, and the only way to reduce the time taken is to reduce the number or size of files, make performance improvements in WP or get a better host.
I only have control over the first option, and I don't think there are any superflous files in Crayon. I had jQueryUI in the first 2.0.0 release, but I've removed it since and I'm using the version included with WordPress. I've been using the jQuery included with WordPress for about a year or so now, and the only other major script I use is Fancybox.
There are a large number of files for languages and they don't change very often, so having delta updates for plugins much like they do for core WP would be nice.