There's certainly no technical flaw in MeGUI that makes it unsuitable.
As far as easy to use, I personally find that gui solutions can be easier at first, but then once you've gotten an idea of what you want to do and how you want to do it, they make you jump through needless hoops.
My batch setup requires me to set up one normal avs script, one youtube avs script, and a few parameters in a project file, and then it automatically spits out:
vorbis audio
aac audio
flac audio
normal encode (original res, 4:2:0, flagged AR, dedupped)
hi10 encode (original res, 4:4:4#10, flagged AR, dedupped)
512 encode (lancos resize to calculated AR, 4:2:0, no dedup)
youtube encode (resize by avisynth, decimate by avisynth, 4:2:0, no dedup)
normal mux (normal+vorbis in mkv)
hi10 mux (hi10+vorbis in mkv)
512 mux (512+aac in mp4)
youtube mux (youtube+flac in mkv)
Each output file is given the project name I specified, plus its type, plus the CRF that it was encoded at. When I audition the results, if I don't like one I can just change the CRF in the project file, and it automatically redoes only what's necessary and gives me the new output (with different name by CRF) to compare with the previous one.
Now, was this complex to set up? Maybe. Took a decent amount of time to hammer everything down. Now that it's done though, I'm not clickety-clacking through UIs all day. Plus it's easily extensible. Adding things like
Turska's 4:4:4 mkv workaround is trivial and doesn't increase encoding effort required at all. Even a whole extra encode, say, WebM, wouldn't be that bad.