I have now entered the phase where I'm asked for the yomikata and have done quite some practice. Here are some things that bother me about the current system and that may be improved:
1) Testing English > Yomikata By now I have the feeling this is not helping me much, because I rather tend to link the yomikata to the English. I would prefer a Kanji > Yomikata way, where the English is either not shown at all or only in small font on the upper edge.
2) Learning all the readings So far the system accepts only one reading as correct and then skips to the next Kanji to test. I (and probably many others) tend to be lazy, so entering the same Onyomi every time and not bother about the rest that one does not recall immediately. In principle the current way is ok, because testing all yomikata individually would immensly blow up the training sessions and is too tedious. However, I would like to see all possible reading pop up as a hint once you type one correct reading.