As far as study type '1', I think it's really quite a waste of time to study kanji and their readings in isolation. You can memorize all 5 readings for one kanji and all 3 readings for that kanji, but when you encounter a compound of the two characters together you now have 15 possible ways to pronounce it... which doesn't help at all. That kind of study is a trap to be avoided.
If you wanted to do that -kind- of study anyway, you can improve on it by studying kanji with vocabulary that uses each reading. Of course now you're studying vocabulary in isolation which can be misleading for all but the simplest words. I think it would even better to limit yourself to one common word per kanji if you were doing this kind of study.
I highly dis-recommend any of the apps (and they are legion) that give you kanji flashcards for this first style of learning. They don't exist in huge numbers because people like this style of app, but rather because it's
really, really easy to consult the free KANJIDIC database and do random flashcard drills on the same basic information.
If you want a flashcard app (and I think flashcards are very useful), then I strongly recommend using the 'smart' flashcards of a Spaced Repetition Software (SRS) rather than simple 'dumb' flash cards. Anki
Anki - powerful, intelligent flashcards is the one that I use and is pretty popular, but there are others (Memrise, Surusu, etc.) The important feature these programs have in common is that they show you cards you get wrong -more often- so that you can memorize them, and words that you get right -less often- so that you don't waste time reviewing material you already know.
I think your study type (2) is perfectly valid and is in fact more or less what a lot of people do.
The third way of studying is to use a system like Heisig's Remembering the Kanji (which I used and rather like) or KanjiDamage. In any case the goal here is to learn to write and/or recognize the character and tag it with an English (or your native language) name to associate it with. For those of us who early on found the kanji completely impossible jumbles of lines that could never be distinguished, this kind of system is indispensable.
For people who can just look at a character a few times and forever after reliably recognize it among similar characters that may only differ by a stroke or two.... such systems seem like a waste of time. Not all of us are fortunate enough to have such a memory though, which is why Heisig continues to be popular and other similar mnemonic systems like KanjiDamage are appearing.
Hopefully that helps you understand all your options.
がんばって!