Mnemosyne has a simple, Zen-like interface. There are very few options, but most of what you need is there. Some people may want more buttons-- for example, there's no way to bold or italicize text within the interface; instead, one has to type the HTML tags. This is not difficult but can be intimidating for new users. On the other hand, the program couldn't be more simple to use and get started with.
I really like that Mnemosyne shows the category at the top of the question in a separate bar. Since it uses a small font and is on a different colored background, I rarely notice it, but if I am confused as to where my question came from (it happens once in awhile), I can glance up and the category will give me the clue I need.
I have poor eyesight, and kanji are finely detailed, so I like to make my text really big. On Mnemosyne, it's easy to increase the global text size, and the window has little information on it so you can fill your whole screen with kanji if you want. Unfortunately, the current version does not support scrollbars (!!!), so if you make the text too big (or just have a few long sentences on a single card) it won't all fit on the screen, and you'll have to manually adjust the screen to see it. This is a major annoyance.
Anki has lots of features, but the interface is streamlined and fairly well organized. Although it's not always immediately apparent how to do things, after playing around for a few minutes you can usually figure it out. However, Anki does employ confusing terminology (cards, facts) when you first start using it.
Like Mnemosyne, you can globally control the font in Mnemosyne, but Anki goes one better: you can set different font sizes for different types of cards. That means the vocabulary you practice writing with can be a bigger than your cards that have sentences and conversation samples. This is a great feature.
But, I have a few problems with Anki's basic question and answer mode. Most of these problems can be fairly easily fixed by reconfiguring the program, but I think it's worthwhile to take a look at the defaults, since the default experience is the one that greets every new user.
First, it's hard to distinguish between the question and the answer if you look away from the screen for a second. In Mnemosyne and SuperMemo, there's a tiny bar between question and answer; in Anki, there's just a little white space. Since you can enable this bar in Anki, if you use the program I recommend doing so.
Second, I don't like that once you answer a question, when it shows you the next question at the top of the screen it also shows the first line of the old question, the same for the answer, and then also a little congratulatory statement and a confirmation of when the card will be shown again. This feature really slows me down, because when I do my cards, I get in "read everything quick mode", and constantly seeing the last card at the top of the screen means my eyes will pass over it and try to read it almost every time. Since Anki supports undo of mistakes (unlike Mnemosyne), I'm not sure why this "feature" is there. Again, this is an annoyance with every single card I do.
Third, by default the buttons are vertical rather than horizontal, which takes up far more screen space than Mnemosyne, and causes scrollbars unnnecessarily. Thankfully, this can be changed in the preferences.
Last, Anki does not show the category of the question by default; you'll have to enable this yourself. So, on the one hand, none of these complaints are very major, since you can reconfigure Anki. On the other hand, you have to reconfigure Anki, when what you really want to do is get started using the program.
But Anki's interface problems are nothing compared to SuperMemo's, which has one of the worst interfaces I have ever used in any program.
The basic interface of SuperMemo is quite simple and likeable. However, although getting started with the program is relatively easy, once you want to use some of the advanced features you should be prepared for a frustrating experience. The SuperMemo interface was established more than a decade ago and it feels like new features were just hacked on, rather than gracefully melded into the program.