Personally, I find the interface is extremely functional; the ability to have deck hierarchies to be a massive feature, not a bug; the WYSIWYG being the default being obvious given the intended audience, but one can still easily edit a textfile and import it or edit in html mode directly if desired; converting something into latex math is as simple as enclosing it in "[$] ... [/$]" and hardly the nightmare it's portrayed as; and finally potentially hacky plugins is a feature, not a bug: occasionally you have a very specific problem and some kind soul creates a solution for you, which may be functional but not the most aesthetically pleasing. That's fine. Anki is a bazaar, not a cathedral, and plugins have ratings and reviews which you can consult if necessary.
I have tried many different flashcard solutions, including hacky text-based ones, and I always return to Anki. Despite the fact that most other tools in my stack that I swear by are terminal-based.