Answer
The prophecies about the twelve tribes, like all other prophecies, are conditioned upon God's covenant. Notice that most of the negative prophecies include explanations for their negativity: they are rendered partially as judgment for covenant violations, and partially as warnings about what awaits them in the future if they do not change their ways. The positive prophecies are also conditioned upon covenant obedience (cf. Jer. 18:1-10).
Moses' presentation of the prophecies is designed to teach the different tribes how to relate to one another and how to get along in the Promised Land. Judah was to be the ruling tribe, even though Judah was not the firstborn. This is probably why specific explanations are given regarding the disqualification of the older brothers (Reuben, Simeon, Levi). Judah's leadership typified David's dynasty, and ultimately Jesus' kingship (David and Jesus were both of the tribe of Judah).
Some of the prophecies worked to motivate change in the people to whom they were directed. Specifically, some the descendants of tribes with negative prophecies heeded the warnings and changed their ways. For example, Moses and Aaron, preeminent in their day, were of the tribe of Levi. Though Jacob did not enter into Levi's counsel (because Jacob died), God himself entered into Moses' counsel and united his glory with Moses' assembly. God spoke face to face with Moses (clearly entering into his counsel), and he showed him more of his glory than he showed anyone else (Exod. 33:18-34:35). Also, it was under Moses' leadership that God's glory came to dwell in the tabernacle (Exod. 40:34ff.). The tribe of Levi as a whole did not receive an inheritance in the Promised Land, but this was not a bad thing -- the Lord himself was their inheritance, as were the tithe and other offerings (Num. 18:19-21). When God excluded them from an inheritance in the Land, he did not appeal to Jacob's last words, but to the fact that they had received the tithe as their portion (Num. 18:24).
Also, it is worth noting that most of the prophecies are quite vague. They could be fulfilled in innumerable ways without trouble, especially given the metaphoric nature of the language. Also, because all prophecy is fundamentally conditional, God could alter, revoke, mollify, delay, etc., the fulfillments if he so desired.
Ultimately, the point of the prophecies was not to reveal specific, unchangeable, future events, but to motivate the people to: pursue the positive blessings by continuing their obedience; avoid the negative curses by ceasing their sin; and follow God's plan for each tribe in the Promised Land.
Answer by Ra McLaughlin
Ra McLaughlin is Vice President of Finance and Administration at Third Millennium Ministries.