Why was Saul rejected when he described himself the same way Gideon did?

Because smallness is not the qualifier. Election is.

The parallel between Gideon and Saul is one of the Hebrew Bible's most striking near-repetitions. Both men describe themselves in almost identical vocabulary before being called.

Gideon, when the angel finds him threshing wheat in a winepress (Judges 6):

"Behold, my clan is the weakest (דַּל, dal, H1800) in Manasseh, and I am the youngest (צָעִיר, tsa'ir, H6810) in my father's house." — Judges 6:15

Saul, when Samuel comes to him (1 Samuel 9):

"Am I not a Benjaminite, from the smallest (קָטָן, qaton, H6996) of the tribes of Israel, and my clan the least (tsa'ir, H6810) of all the clans of the tribe of Benjamin?" — 1 Samuel 9:21

Saul's self-description is arguably stronger than Gideon's. He uses both H6996 qaton (tribe-level smallness) and H6810 tsa'ir (clan-level smallness) in a single verse — the same vocabulary Gideon stacks across dal + tsa'ir. If any reading of the pattern said "God chooses the small because smallness earns the choice," Saul should be the climactic case.

Saul is not. Saul is anointed king (1 Sam 10:1), reigns for a time, and then is rejected:

"And Samuel said to Saul... 'You have rejected the word of the LORD, and the LORD has rejected you from being king over Israel.'" — 1 Samuel 15:26

Two kings described themselves with nearly identical smallness vocabulary. One delivered Israel (Jdg 7–8); one was rejected. The near-repetition is the text's own guard against a certain kind of misreading.

The misreading would go like this: "The pattern of Genesis through Samuel — Isaac, Jacob, Ephraim, Gideon, David — shows that God elevates the small. So smallness is a spiritual virtue. If you are small in your own eyes, you are the kind of person God chooses." The Saul case directly contradicts this. Saul was small in his own eyes. Saul was rejected.

What the text teaches is something more careful. God chooses whom he chooses, and he chooses, visibly and repeatedly, the small. But the choice is the choice; the smallness does not compel it. The qualifier is election itself.

The text of 1 Samuel 15 explains Saul's rejection in disobedience-terms: Saul spared Agag and the best of the Amalekite livestock against YHWH's explicit command (1 Sam 15:3, 9, 22–23). Samuel's summary:

"Behold, to obey is better than sacrifice, and to listen than the fat of rams. For rebellion is as the sin of divination, and presumption is as iniquity and idolatry. Because you have rejected the word of the LORD, he has also rejected you from being king." — 1 Samuel 15:22–23

What began as smallness ended as rebellion. The vocabulary of self-description at 1 Sam 9:21 did not prevent the disobedience at 1 Sam 15.

The Apostle Paul captures the principle at Rom 9:16: "So then it depends not on human will or exertion, but on God, who has mercy." The election precedes the response. Smallness does not produce election; election is what God does with smallness. Saul's smallness did not save him; Gideon's did not make him. YHWH said to Gideon, "I will be with you" (Jdg 6:16). That is the whole of the call. Saul did not continue in that commitment.

The Saul case is why the pattern has theological weight rather than merely sentimental appeal. The Bible repeatedly places the smallest of the smallest in a place of honor — Jacob over Esau, Gideon over the Midianite army, David over Goliath, Bethlehem Ephrathah as the Messiah's birthplace. The text is not saying smallness is earning those elevations. The text is saying God chose those particular small ones, and the fact that he chose the small rather than the great is itself the teaching.

This is why Paul writes in 1 Corinthians 1:29: God chose the foolish, the weak, the low-born "so that no flesh may boast before God." If smallness were the meritorious qualifier, the small could boast of their smallness. The fact that Saul's smallness led to rejection keeps the pattern from becoming a new basis for self-commendation. God chooses whom he chooses. Being small does not change that.

For the full treatment — including the Gideon paradigm, the whole seven-figure sequence from Isaac to David, and Paul's apostolic summary in 1 Corinthians 1 — see the study The Youngest Chosen.