The grand staff is really a single giant clef with the middle line missed out for clarity, and some extra space added around it to allow for leger lines.
Your system would need extra legers above/below the clefs, so it wouldn't be an obvious improvement.
Coloured note heads are better at conveying pitch than note shapes - which are already used in percussion notation. But coloured note heads cost a lot more to print, and scores are expensive enough as it is.
Having notation that is consistent across all instruments, not just piano, is a good thing.
I doubt anyone would duplicate current notation if it was designed from scratch today. But like a lot of things - including CSS and HTML - it's a mass of accreted compromises with a massive existing user base.
No one is going to re-notate centuries of music with a new system, no matter how much more logical it is. It's not going to happen for the purely practical reason that most music will still be in the old system, and musicians would still have to learn that system to play it.
Shape notes are used in singing traditions such as Sacred Harp and Christian Harmony to help singers find the right pitch. It works very well. I don't know if anyone uses them for instrumental music.
My biggest problem with music notation is it being centered around the key of c major. When ever critiques of current music notation come up I like to bring up the janko keyboard. It has an isometric layout which means that any interval will have the same shape no matter the starting pitch. With this layout if you learn a major scale in one key you've learned it for every key. Transposing from one key to another is just shift your hands. I haven't seen an alternative music notation system which has advantages like this while still being compact and readable.
See here for some experiments in attempts to improve the situation: http://musicnotation.org/
This ends up being particularly helpful when reading scores, because you can see at a glance where each instrument is playing in their register. Who's playing the melody? Just look for the notes that are highest up on the staff. Notes that are high in an instrument's register tend to have more high frequency partials and stand out in the mix.
Interestingly enough, other clefs do already exist. The "C" clefs (alto and tenor clef) identify middle C and simplify note reading for instruments that have atypical tessiturae.
Even though the prospect of initially having to memorise only half of the notes, this amount of time is trivialised by the time it takes to get your fingers to respond by hitting the right note fluently.
Also, even easier than your proposed extra line would be to double the treble clef and indicate it's to be played 1 octave lower. I haven't seen this in mainstream teaching materials, and I surmise this isn't done because of the trivial time saved in the long run [1].
As for your second point: I strongly feel that for complex keys muscle memory and interval awareness trump extra visual information. In other words: if you are playing in a complex key, you should already have this awareness, and if you don't, you shouldn't be playing in this key.
There might be an interval between starting to learn a key, and becoming familiar with it, where extra information regarding the colour of the key might be useful, but I'm unsure if it outweighs the extra visual clutter, especially when considering that, when mastering a complex key, one presumably would have already mastered less complex keys, and already has a developed sense of muscle memory and considerable interval awareness.
[1] I have seen notes that have the value of the note imprinted on them. These are used mainly in children's teaching material, and are dropped fairly quickly after the concept of note-key correspondence is established.
There’s a new notation whose name I’m forgetting which resolves this problem — I’d expect it to make sight reading significantly easier to learn.
Regarding your first suggestion, there is actually a relation between the two staves: the ledger line above the bass clef and below the treble clef represents the same note: a middle C. Also, keep in mind that, the "larger" the staff, the harder it is to recognize quickly the note to play. It's not a bad idea though, and worth exploring!
Another improvement, especially for piano music is to make the white/black key indication carried in the note shape/head. right now the note head carries duration information. it could also include whether it's a black key or white. this is useful especially for complex keys with many sharps/flats. this way whether you're in C major or Ab Minor, you dont have to constantly remember which notes are accidentals. sure, youre supposed to learn the scale and remember (including all the cancellations, double sharp/flats), but it's massively easier if this useful info is carried in the note shape. eg: square note head = black, triangle = white.
sorry for the rant!