That could work.

Skritter is a bit half-hearted with tone colors. It's allowed in the web app as an option, but it's confusing, since colors are already used to indicate the four levels of grading: don't know, so-so, got it, too easy. And tone colors are not available in the mobile versions, I think.

Personally I like tone colors, and wouldn't mind giving up grading colors for tone colors to work better.

Anyway your suggestion could be done now for the web app, where as you say the definitions can indeed be very ambiguous, even in the info window:
http://www.skritter.com/scratchpad?word=与

What they use is a semicolon between different definitions with the same pinyin and a new line for an other pronunciation.

I agree that it is very difficult to see on the iOS app. I've suggested to them before that they make it more clear, but seemed to think it was good enough already.

I also think they should indicate in some way if one simplified character maps to multiple traditional, which definition (and pinyin) belongs to which traditional.

Compare with Wenlin:
112 与(F與) [yǔ] and [yù] 参与 cānyù participate in [yú]
与[與] ¹yǔ* {B} b.f. ①give; offer 赠与 zèngyǔ ②commend; support; assist 与人为善 yǔrénwéishàn ③get along with 易与 ³yìyǔ ④wait ◆cov. with; to ◆conj. and; together with
与/预[與/預] ¹⁰yù {E} b.f. participate 参与 cānyù 与会 yùhuì 预政 ¹yùzhèng
欤/与[歟/與] ¹⁹yú b.f. (classical final particle expressing surprise/etc.) 猗欤 ³yīyú 猗欤盛哉 yīyúshèngzāi

I am a huge fan of colours too. It would be nice if you could change the colours to your own taste though.

I would like to be able to edit the pinyin in the same way I can edit the definition. Often, there are more pinyin entries than there are groups of meanings. Often, some of the included pinyin entries represent old or even archaic forms.

With respect to the contributors of the database, quite often the definitions are overly generous. As someone who is not a native English speaker but nevertheless fluent enough to fool native speakers into thinking I am, I can tell that they are written by an English speaker to cover a wide variety of English words that are approximately equivalent.

(Sometimes this is an untended consequence of one simplified character representing two or more traditional characters, but often not).

While this is great for looking up the meaning of something, I find it incredibly wasteful for learning vocabulary. A word that has six meanings listed takes me much more than six times longer to memorise. I'd much rather learn one or two very high frequency definitions, and add others as I encounter them in context of a conversation or reading. The same applies for pronunciation.