I have to agree with Jak here. I spend equal amounts of time playing in various situations because they all have their challenges.
-Practicing on acoustic guitar will strengthen the fingers greatly and help you to project/play with volume and dynamic.
-Clean electric guitar will expose the type of flaws most of you are describing like unsynchronized picking and fretting causing dead notes and inarticulation. There is also a slightly greater sensitivity than playing on acoustic guitar especially if you have some compression or EQ in your chain. This requires a lot more “touch” or “feel” at times, but not always.
-Distorted electric practice is essential because like Jak said, this will magnify the lesser discussed flaws in your playing like poor palm muting technique, artifact control(controlling unwanted noise), non targeted string attack(accidental hitting of unwanted strings either by picking or fretting hand), to name a few.
I play a lot of acoustic because I really enjoy Gypsy Jazz and have a lot of catching up to do because of my late start so I tend to tip the scales in favor of that, which actually hurts my electric guitar execution. I say execution because I’m not talking about harmony or theory. Gypsy Jazz has opened up a whole other world or lexicon of harmony and melody which has helped increase my musical palette. By execution, I’m referring to the way I handle the electric guitar such as the way I pick, palm mute, or string mute with my fretting hand. These extremely fundamental approaches to playing guitar vastly differentiate between all 3 platforms.
And getting into FX is a whole different ball of wax that should be treated as an entire craft of it’s own.