Ah, the joys of modifying minions. . .
Here are a few points from my experience from similar games:
1) Increase the base stats: This can become a slippery slope of every-growing numbers, but if you need it, it's there. Raise the stats for the important skills, increase Wounds, arbitrarily raise soak. . .do what you have to.
2) Give them a few perks. Let them have a few talents that they normally wouldn't have that will make them formidable. Allow them to do something that the PCs won't have access to but is still fair (like the Adversary talent, for example).
Other perks can include a Defense increase as long as they are still in a group.
3) Play them smart. Have the "squad" break apart and put the group in a crossfire, and throw in a boost die or two for that as well as the standard bonuses for the minions doing their thing.
4) Add a leader. This can be tied to "Play Them Smart," but you can add other bonuses.
Is it the 501st being lead by Vader into battle? Allow them all to upgrade their pool once for the sheer leadership, admiration, or the fear of failure.
Is it a smaller group lead by a trusted luietenant? Maybe a boost die is in order.
5) Make Leaders REALLY worthwhile. Perhaps allow the group to use certain Advantages that the Leader has if, and ONLY if, the leader is still alive.
Does the Leader have Armor Master? Then everyone gets it! The same can be true for things like Adversary and the like.
6) Use the minions as Support for a "leader." Want to ensure that you Stormtrooper Sergeant is going to hit and hit hard? Instead of the usual boost die, allow an upgrade for every Minion involved in the roll with the appropriate skill. Brutal, but effect, and means a squad of Stormtroopers becomes even deadlier than they already are.
Just my thoughts and theories on the topic. Enjoy!