UPDATE: A year after the writing of this post, I totally changed my position regarding Beitin and Bethel.
Bethel was located in the hill country of Ephraim (Judges 4:5) and in Benjamin (Josh 18:22). It was said by both Jerome and Eusebius to be at the 12th milestone from Jerusalem, but Beitin (the conventionally accepted Bethel, LB IIB fortress at 31°55’37″N, 35°14’20″E) does not fit, either by size, archaeology, or distance.
Firstly, archeologically, Beitin only had strong activity beginning in the Iron IIB; the 8th century BC. Throughout the entire period of early Iron IIA and late Iron I (from Saul to Omri), there was hardly any sort of settlement at Beitin! Even in the days of Jehu, there is no evidence of any great city at Beitin. After the 8th century, Beitin remained a poor village until the Hellenistic period.
Secondly, Judges 4:5 makes far better sense if a Ramah is placed at Ramalla and Bethel placed at Bireh (there are over five miles between er-Ram, certainly a Ramah, but certainly not the one mentioned in the verse, and Beitin [remember the existence of Mizpah]). Ras et-Tahuneh, 31°54’30″N, 35°12’44″E, the most likely candidate for Bethel’s high place, contains 40% Iron II shreds. We can therefore assume Bethel as el-Bireh, since, if it is not Bethel, it is not mentioned in the Bible (Beeroth is at Biddu according to Eusebius’s distances and the implication of other Bible verses, and at Khirbet al-Burj according to Finkelstein, which, while a fine Iron II site, is too near Jerusalem to fit Eusebius’s distances). Since Bethel was in Benjamin, Beth-Aven must be interpreted in Joshua 18:12 as being north of Bethel. Since Ai was “near” Beth-Aven, Beth-Aven should preferably be to the east of Bethel/Bireh. Beitin is the only site with Iron II pottery Northeast of Bethel that is west of Michmash (1 Sam 13:4). It is therefore the best candidate for Beth-Aven. Since there are only two archeological sites that were ruins during Iron II in the vicinity of Beitin, Kh. Maqatir, 31°54’54″N, 35°14’58″E, and et-Tell, et-Tell being excluded due to its being larger than Gibeon in Joshua 10:2 (Gibeon was 16 acres. et-Tell was 27), Khirbet Maqatir is the only candidate for Ai. This is supported by Genesis 12:8, which says there is a mountain between Bethel and Ai (obviously, the one at 31°54’47″N, 35°13’49″E). Burj Beitin, the conventionally accepted “mountain” is not even a hill, but a modest ridge, and was only inhabited in the Byzantine-Crusader era. The most likely locations of Iron II and Persian Ai are Sites 205 (31°54’45″N, 35°14’51″E) and 204 (31°54’33″N, 35°15’4″E), respectively, on the previously linked Benjamin Survey. Khirbet Nisya, 31°53’48″N, 35°13’45″E, is therefore Zemaraim.