The following is how Abarbanel parses the list:
והתחיל מראובן כי הוא היה הבכור גם הוא ראש דגל. ואחריו שמעון שנולד אחריו והוא ג״כ בדגלו. ולפי שלא הלך מרגל משבט לוי זכר אחריו יהודה כפי תולדותם ושהוא ראש דגל כמלך בגדוד ואחריו הנכבד מהחונים עמו בדגלו והוא יששכר ואחריו אפרים שהוא ראש דגל ואחריו הנכבד מהחונים בדגלו והוא בנימין. ואחריו זבולון כי הוא בן לאה והיה נשאר מדגל יהודה, ואחריו מנשה שהוא הנשאר משבט [ממחנה?] אפרים ואחר שזכר בני הגבירות זכר בני השפתות רוצה לומר אותם ג׳ שהיו בשבט דן. ונשאר גד באחרונה
So, it goes:
- The greater two from degel Reuven.
- The greater two from degel Yehuda.
- The greater two from degel Efraim.
- The remaining from the above two camps.
- The three from the camp consisting of all the b'nei hashfachot.
- The only remaining ben shifcha: Gad.
Now, because this seems only ever so slightly better than a randomly ordered list, Abarbanel finishes:
והיה הסבה לכל זה מה שזכרתי ששמר בהם הקדימה והאיחור כפי מעלתם בעצמם וכמו שכתב הרמב״ן
But, perhaps the above order is not so random if we incorporate an idea from John Gill's Exposition of the Bible:
and the several tribes are mentioned, not according to the order of the birth of the patriarchs, nor according to the dignity of their mothers that bore them, but, very likely, according to the order in which they were sent, two by two, to search the land; for had they gone all twelve in a body, they would have been liable to suspicion
This is not a far-fetched idea, as we do see that Yehoshua sent two spies, possibly for this reason, and we do find several commentaries back when Yosef's brothers argued that they were not spies explaining their argument based on this same idea.
So, if we group the meraglim two by two, we get something relatively coherent:
The only thing that seems odd to me about this order is that I would have said that "the greater two from degel Efraim" are Efraim and Menashe, as that follows their order from Bamidbar 2. It could be, as you suggested here, that they wanted to sent Gadiel ben Sodi and Gadi ben Susi together because their names are similar, but that seems far-fetched to me. More likely, in my opinion, is that really Efraim and Binyamin are the greater two of that camp, just in Bamidbar 2 we put Efraim and Menashe together under the "Yosef umbrella" and always juxtapose them.