Maybe it's not an issue on Lunatic, lol, I was a scrub on Hard. Juggernauts are a problem but I think they can be mitigated in much better ways than just making units ignore them, which is especially problematic since they won't ignore a unit they can scratch but effectively leave untouched. In Hard it was a gigantic pain in the ass that Xander would just get ignored on a large number of enemy phases and playing around it didn't make things interesting, just boring and frustrating, especially since it's different than AI behavior before. I mean, Ryoma never has this issue because he can be hurt, but I would say that he is a much, much more problematic super unit, it's just that he "can" take damage but won't because of Vantage/Astra/Guard Stance/dodgetanking.
Better ways to mitigate this is by diverse enemy compositions with mixing a large amount of magic and physical damage and adding effective weaponry often enough, or by making enemy density thick enough that you can't just have 1-2 juggernauts handle everything. FE6 does this really well with diverse threatening enemies (Wyvern Lords are threatening to basically anyone, plenty of status staves/siege tomes) and using the siege objective to the best the series has ever done. If side objectives are also worthwhile, it can demand that the player be forced to use multiple strong units instead of relying on one juggernaut to power through everything. The tradeoff to this in FE6 is that unit balance is awful, but even a stupidly OP Milady and Perceval weren't enough to just steamroll my way mindlessly through the lategame and I had to use many more units that weren't as ridiculous (Shin, Cecillia, Fir (>.>), Rutger, Tate and her sister, Niime, Saul) to do a lot because Milady and Perceval couldn't do everything at once or handle every situation.