Your examples were stacked against JJ because you always included precisely one ace, one king, and one queen among the opponents' hands. That will not always happen.
To see whether AKo is stronger than 22, you don't put them together in the same hand, where 22 is a slight favorite. You see how well they play against other hands, where AKo greatly outperforms 22, e.g., AKo is a big favorite over J9o, which is a favorite over 22. If you want to compare JJ with KQs, here are some comparisons.
Equity against 55:
JJ: 80.5%
KQs: 49.5%
Equity against KTo:
JJ: 71.3%
KQs: 74.6%
Equity against A6s:
JJ: 68.5%
KQs: 43.0%
Equity against AKo:
JJ: 56.9%
KQs: 29.6%
Equity against KK:
JJ: 18.5%
KQs: 13.9%
Equity against "any face card":
JJ: 70.3%
KQs: 61.4%
Equity against a random hand:
JJ: 77.5%
KQs: 63.4%
Equity against ATs, 88, and T9o:
JJ: 49.9%
KQs: 32.3%
Equity against T4o, 32s, and 96o:
JJ: 58.6%
KQs: 41.2%
Equity against AA, TT, and 65s:
JJ: 16.8%
KQs: 13.5%
It looks like JJ wins more in almost every situation, but the above figures are just hot-and-cold. Is it different in practice? No. JJ wins 0.86 BB/hand in limit, according to PokerRoom's
stats. KQs wins 0.39 BB/hand.