Hi lanthas,
I understand all that, and recognise it is not for everyone. Different people will want to tackle different aspects of learning kanji in different orders, and I personally like the Heisig idea of making kanji familiar and meaningful as symbols prior to actually learning the Japanese that uses those symbols. I know that some people can't stand the idea. The hand-writing aspect is primarily to encourage motor involvement in the learning process because it improves recall - multichoice is so much less engaging. Because the app replaces finger strokes with neat versions of the strokes, it does not actually require much care in terms of actual hand-writing. I used an early version of this app to learn about 500 kanji and didn't find that the stroke order presented any particular challenge. Once you know the basic principles of stroke order, the natural intuitive order is correct in most cases, so that becomes a side issue as well. You can also enter multi-stroke combinations via picture selection, so you don't have to trace out each stroke if you don't want to.
To use your example of 何 and 伺, I cannot imagine ever confusing them having drawn them both. Whatever tips you used for distinguishing them and other lookalikes can be entered in the mnemonic notes for each kanji, along with any other usage notes of interest, such as the material at KanjiDamage.
The main value of the app is that it makes it fairly easy to learn 2000 kanji in a few weeks, letting you get on with the rest of your learning. If you use Japanese prompts, instead of English keywords, you also pick up about 2000 words of vocab along the way, but that's a side benefit.
Cheers,
Torrential.