System opening disadvantages: Sometimes not the most aggressive openings. Can lead to stale opening play. That is, you get used to "not thinking" about the first seven moves or so.
I think the one major disadvantage is that whilst you are on 'auto pilot' to some extent, you may not process that your opponent is setting up a threat or advantageous position, and continuing with your 'system' might get you into trouble.
It's why I actually dont like recommending 'system' openings to beginners as I think it's critical they build the habit of processing and responding to each move as they see it. Too many beginners get caught off guard by an attack they didn't see, due to their 'auto pilot' system building replies. For intermediate players and above, I think system openings are fine.
Moosemouse. Your original post on white systems and all your comments have been FANTASTICALLY helpful for my chess development. Ignore the pedants. I was totally new to chess one year ago and am now 1100+ on chess.com. I may never get above 1400 as I came to chess at 48, so CZ, English Botvinnik and BM gambit are terrific. And fun! Thanks once again for your excellent posts. 😀