Great reading your thoughts on this!
I also reacted at first when I saw that they labeled it Funkadelic and that it should’ve been better with GC & the P-funk All Stars or something. But, just like @OooBooBeeDoop, I feel they experimented more when they used the Funkadelic name, and that fits Shake the Gate.
Actually, I recently started to think about if maybe P-funk All Stars wasn’t ideal either. To me, the P-Funk All Starts was the band up until maybe How Late…, and after that (or at least since STG/MFD) the new generation started to tour and record. But I don’t know, one could argue that it’s like an all star team and that the players change all the time… But at the same time I now feel that it doesn’t matter so much, I’m just glad to get the music.
When there’s a 33 track release, there’s bound to be some tracks that you don’t like as much. And always when there’s a double or triple album, you’ll get people saying (including me) that it would’ve been the bomb if they only made it a single disc. But since everybody have different opinions on what should be on that single disc, it would probably not have been the tracks you wanted anyways. So it’s probably good that they didn’t trim it.
The idea with three separate albums with better flow is interesting. But then they wouldn’t have that one album with 33 tracks because it was 33 years ago thing. 
These are my favorites from Shake the Gate (you can probably see a pattern 
):
Baby Like Fonkin’ It Up
Ain’t That Funkin’ Kinda Hard on You (mix)
In da Kar (though I like the efunk and fsq mixes the most)
Radio Friendly
First Ya Gotta Shake the Gate
Boom There We Go Again
Dipety Dipety Doo Stop the Violence (despite the funny title. free alterations!)
Medicaid Fraud Dogg. I feel that MFD had a better flow/more consistent. And you could argue that the added horns fits in with the Parliament name. My favorites from from MFD are:
Medicated Creep
I’m Gon Make U Sick O’me
Antisocial Media
On Fire
Riddle Me This
No Mos
Medicaid Fraud Dogg
Insurance Man
Out of these, On Fire is the favorite. I can play that one on repeat all day! 
I feel MFD is the stronger one of the two. I could easily add a couple more track to the list above.
Btw @Seventieslord, your P-Funk All Stars disc has the same track list as your George Clinton disc. 