In general, official client tries to do too many things at once. In the result, the code base is huge -- too big to be easily audited; it's also proven that it's likely to have a lot more bugs. On a similar note, letsencrypt-auto, the default installation method, pulls in Apache plugin with all of its dependencies. And so on, and so forth...
At the same time standard modes of operation are well hidden and/or difficult to configure. For instance, running the official client without root is technically possible, but let me know how much time it took you to figure this out ;). Likewise, scripting is pretty much impossible, because the CLI tends to ask interactive questions... "webroot" plugin is probably the only plugin that could be made into non-interactive mode, and again you have to be knowledgeable enough to figure out all necessary flags.
simp_le tries to takes the best from the official client ("webroot" plugin -- not stealing, I authored that plugin myself) and adds some missing features that IMO should be the standard. E.g. you can just just put `simp_le --some --flags && this_command_will_be_run_only_if_cert_was_renewed_eg_restart_nginx` into your crontab -- this mode of operation is simply not possible with the official client.
NB You can also turn simp_le into a standalone binary (~8MB) using built-in PyInstaller setup [1] and distribute to your machines without having to install any dependencies (even Python) :)
I hope that answers your question. You can also catch me on #letsencrypt, or better yet #simp_le (both at Freenode).
[0] https://github.com/kuba/simp_le#manifest [1] https://github.com/kuba/simp_le/tree/master/pyi